MiMeDB: Showing metabocard for (KDO)2-lipid A (MMDBc0032104)

Record Information

Version

1.0

Status

Detected and Quantified

Creation Date

2021-11-18 02:02:30 UTC

Update Date

2022-08-31 18:30:33 UTC

Metabolite ID

MMDBc0032104

Metabolite Identification

Common Name

(KDO)2-lipid A

Description

(KDO)2-lipid A is an intermediate in the synthesis of LPS. It has two 3-deoxy-D-manno-octulosonic acid (KDO) sugar residues in place of the core, and has no O-antigen.

Structure

MOL SDF PDB SMILES InChI

      
  Mrv1533005211517282D          

175178  0  0  0  0            999 V2000
   -2.5857    9.2360    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.6897    4.2914    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -8.0674   -9.6323    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.3706   -1.4730    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    7.7108    9.6323    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.3410    7.8404    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7849    9.0378    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8668    4.3504    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -7.7071   -8.8902    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.7986   -0.8785    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
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   -4.1122    7.0477    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
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   -2.3021    2.2420    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
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   -2.6249   -0.6804    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
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   -2.2817    5.8588    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.2744    7.0563    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.6624    1.4998    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.3406   -7.2878    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0528   -0.0859    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
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   -1.2520    4.8680    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
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   -2.5602    0.0745    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.1574   -6.4867    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6800    0.3103    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
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   -1.0232    4.0753    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
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   -2.0976   -0.6085    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
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   -1.9954   -2.0338    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1513   -5.6265    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
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    5.9947    2.6968    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.8072    2.8864    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.5922    3.2912    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8932   -3.4591    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9681   -4.8253    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.8666    0.9048    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.6515    1.3097    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.9830   -7.7621    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.2832   -4.8369    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
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M  CHG  6 120  -1 121  -1 130  -1 132  -1 133  -1 134  -1
M  END

      
  Mrv1533005211517282D          

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 85160  1  6  0  0  0
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 88163  1  6  0  0  0
 95164  1  6  0  0  0
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100169  1  6  0  0  0
101170  1  6  0  0  0
102171  1  1  0  0  0
103172  1  1  0  0  0
104173  1  6  0  0  0
105174  1  6  0  0  0
106175  1  6  0  0  0
M  CHG  6 120  -1 121  -1 130  -1 132  -1 133  -1 134  -1
M  END
> <DATABASE_ID>
MMDBc0032104

> <DATABASE_NAME>
MIME

> <SMILES>
[H][C@@](O)(CCCCCCCCCCC)CC(=O)O[C@@]1([H])[C@]([H])(O)[C@@]([H])(CO[C@]2([H])O[C@]([H])(CO[C@@]3(C[C@@]([H])(O[C@@]4(C[C@@]([H])(O)[C@@]([H])(O)[C@]([H])(O4)[C@]([H])(O)CO)C([O-])=O)[C@@]([H])(O)[C@]([H])(O3)[C@]([H])(O)CO)C([O-])=O)[C@@]([H])(OP([O-])([O-])=O)[C@]([H])(OC(=O)C[C@@]([H])(CCCCCCCCCCC)OC(=O)CCCCCCCCCCCCC)[C@@]2([H])N=C([O-])C[C@@]([H])(CCCCCCCCCCC)OC(=O)CCCCCCCCCCC)O[C@]([H])(OP(O)(O)=O)[C@]1([H])N=C([O-])C[C@]([H])(O)CCCCCCCCCCC

> <INCHI_IDENTIFIER>
InChI=1S/C110H202N2O39P2/c1-7-13-19-25-31-37-38-44-50-56-62-68-92(123)142-82(66-60-54-48-42-35-29-23-17-11-5)72-94(125)146-104-96(112-90(121)71-81(65-59-53-47-41-34-28-22-16-10-4)141-91(122)67-61-55-49-43-36-30-24-18-12-6)105(144-88(102(104)150-152(133,134)135)78-140-109(107(129)130)74-86(98(127)101(148-109)85(119)76-114)147-110(108(131)132)73-83(117)97(126)100(149-110)84(118)75-113)139-77-87-99(128)103(145-93(124)70-80(116)64-58-52-46-40-33-27-21-15-9-3)95(106(143-87)151-153(136,137)138)111-89(120)69-79(115)63-57-51-45-39-32-26-20-14-8-2/h79-88,95-106,113-119,126-128H,7-78H2,1-6H3,(H,111,120)(H,112,121)(H,129,130)(H,131,132)(H2,133,134,135)(H2,136,137,138)/p-6/t79-,80-,81-,82-,83-,84-,85-,86-,87-,88-,95-,96-,97-,98-,99-,100-,101-,102-,103-,104-,105-,106-,109-,110-/m1/s1

> <INCHI_KEY>
DIXUKJUHGLIZGU-OIPVZEHTSA-H

> <FORMULA>
C110H196N2O39P2

> <MOLECULAR_WEIGHT>
2232.704

> <EXACT_MASS>
2231.292339975

> <JCHEM_ACCEPTOR_COUNT>
35

> <JCHEM_ATOM_COUNT>
349

> <JCHEM_AVERAGE_POLARIZABILITY>
249.51514569955197

> <JCHEM_BIOAVAILABILITY>
0

> <JCHEM_DONOR_COUNT>
12

> <JCHEM_FORMAL_CHARGE>
-6

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
(2R,4R,5R,6R)-2-{[(2R,4R,5R,6R)-2-carboxylato-6-[(1R)-1,2-dihydroxyethyl]-2-{[(2R,3S,4R,5R,6R)-5-{[(3R)-3-(dodecanoyloxy)-1-oxidotetradecylidene]amino}-6-{[(2R,3S,4R,5R,6R)-3-hydroxy-5-{[(3R)-3-hydroxy-1-oxidotetradecylidene]amino}-4-{[(3R)-3-hydroxytetradecanoyl]oxy}-6-(phosphonooxy)oxan-2-yl]methoxy}-3-(phosphonatooxy)-4-{[(3R)-3-(tetradecanoyloxy)tetradecanoyl]oxy}oxan-2-yl]methoxy}-5-hydroxyoxan-4-yl]oxy}-6-[(1R)-1,2-dihydroxyethyl]-4,5-dihydroxyoxane-2-carboxylate

> <ALOGPS_LOGP>
5.01

> <JCHEM_LOGP>
22.641770333666667

> <ALOGPS_LOGS>
-4.95

> <JCHEM_MDDR_LIKE_RULE>
1

> <JCHEM_NUMBER_OF_RINGS>
4

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-6

> <JCHEM_PKA>
1.187957935558325

> <JCHEM_PKA_STRONGEST_ACIDIC>
0.5457416156588879

> <JCHEM_POLAR_SURFACE_AREA>
662.3900000000003

> <JCHEM_REFRACTIVITY>
605.1682999999999

> <JCHEM_ROTATABLE_BOND_COUNT>
98

> <JCHEM_RULE_OF_FIVE>
0

> <ALOGPS_SOLUBILITY>
2.62e-02 g/l

> <JCHEM_TRADITIONAL_IUPAC>
(2R,4R,5R,6R)-2-{[(2R,4R,5R,6R)-2-carboxylato-6-[(1R)-1,2-dihydroxyethyl]-2-{[(2R,3S,4R,5R,6R)-5-{[(3R)-3-(dodecanoyloxy)-1-oxidotetradecylidene]amino}-6-{[(2R,3S,4R,5R,6R)-3-hydroxy-5-{[(3R)-3-hydroxy-1-oxidotetradecylidene]amino}-4-{[(3R)-3-hydroxytetradecanoyl]oxy}-6-(phosphonooxy)oxan-2-yl]methoxy}-3-(phosphonatooxy)-4-{[(3R)-3-(tetradecanoyloxy)tetradecanoyl]oxy}oxan-2-yl]methoxy}-5-hydroxyoxan-4-yl]oxy}-6-[(1R)-1,2-dihydroxyethyl]-4,5-dihydroxyoxane-2-carboxylate

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 21-MAY-15   NONE
TITLE     NULL                                                        
COMPND    MOLECULE:                                                   
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   21-MAY-15         0                                  
HETATM    1  C   UNK     0      -4.827  17.241   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0      -6.887   8.011   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0     -15.059 -17.980   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0     -10.025  -2.750   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0      14.393  17.980   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0      -8.103  14.635   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0      -3.332  16.871   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0      -5.351   8.121   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0     -14.387 -16.595   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0      -8.957  -1.640   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0      13.326  16.871   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0      -7.676  13.156   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0      -2.905  15.391   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0      -4.488   6.845   0.000  0.00  0.00           C+0
HETATM   15  C   UNK     0     -12.851 -16.485   0.000  0.00  0.00           C+0
HETATM   16  C   UNK     0      -7.463  -2.010   0.000  0.00  0.00           C+0
HETATM   17  C   UNK     0      13.753  15.391   0.000  0.00  0.00           C+0
HETATM   18  C   UNK     0      -6.181  12.786   0.000  0.00  0.00           C+0
HETATM   19  C   UNK     0      -1.410  15.021   0.000  0.00  0.00           C+0
HETATM   20  C   UNK     0      -5.161   5.460   0.000  0.00  0.00           C+0
HETATM   21  C   UNK     0     -12.178 -15.099   0.000  0.00  0.00           C+0
HETATM   22  C   UNK     0      -6.395  -0.900   0.000  0.00  0.00           C+0
HETATM   23  C   UNK     0      12.685  14.281   0.000  0.00  0.00           C+0
HETATM   24  C   UNK     0      -5.754  11.306   0.000  0.00  0.00           C+0
HETATM   25  C   UNK     0      -0.983  13.542   0.000  0.00  0.00           C+0
HETATM   26  C   UNK     0      -4.297   4.185   0.000  0.00  0.00           C+0
HETATM   27  C   UNK     0     -10.642 -14.989   0.000  0.00  0.00           C+0
HETATM   28  C   UNK     0      -4.900  -1.270   0.000  0.00  0.00           C+0
HETATM   29  C   UNK     0      13.112  12.802   0.000  0.00  0.00           C+0
HETATM   30  C   UNK     0      -4.259  10.936   0.000  0.00  0.00           C+0
HETATM   31  C   UNK     0       0.512  13.172   0.000  0.00  0.00           C+0
HETATM   32  C   UNK     0      -4.970   2.800   0.000  0.00  0.00           C+0
HETATM   33  C   UNK     0      -9.969 -13.604   0.000  0.00  0.00           C+0
HETATM   34  C   UNK     0      -3.832  -0.160   0.000  0.00  0.00           C+0
HETATM   35  C   UNK     0      12.044  11.692   0.000  0.00  0.00           C+0
HETATM   36  C   UNK     0      -3.832   9.457   0.000  0.00  0.00           C+0
HETATM   37  C   UNK     0       0.939  11.692   0.000  0.00  0.00           C+0
HETATM   38  C   UNK     0       2.434  11.322   0.000  0.00  0.00           C+0
HETATM   39  C   UNK     0      -4.106   1.525   0.000  0.00  0.00           C+0
HETATM   40  C   UNK     0      -8.433 -13.494   0.000  0.00  0.00           C+0
HETATM   41  C   UNK     0      -2.337  -0.530   0.000  0.00  0.00           C+0
HETATM   42  C   UNK     0      12.471  10.213   0.000  0.00  0.00           C+0
HETATM   43  C   UNK     0      -2.337   9.087   0.000  0.00  0.00           C+0
HETATM   44  C   UNK     0       2.861   9.843   0.000  0.00  0.00           C+0
HETATM   45  C   UNK     0      -4.779   0.139   0.000  0.00  0.00           C+0
HETATM   46  C   UNK     0      -7.760 -12.109   0.000  0.00  0.00           C+0
HETATM   47  C   UNK     0      -1.269   0.579   0.000  0.00  0.00           C+0
HETATM   48  C   UNK     0      11.404   9.103   0.000  0.00  0.00           C+0
HETATM   49  C   UNK     0      -1.910   7.607   0.000  0.00  0.00           C+0
HETATM   50  C   UNK     0       4.356   9.473   0.000  0.00  0.00           C+0
HETATM   51  C   UNK     0      -3.916  -1.136   0.000  0.00  0.00           C+0
HETATM   52  C   UNK     0      -6.224 -11.998   0.000  0.00  0.00           C+0
HETATM   53  C   UNK     0       0.225   0.209   0.000  0.00  0.00           C+0
HETATM   54  C   UNK     0      11.831   7.623   0.000  0.00  0.00           C+0
HETATM   55  C   UNK     0      -0.415   7.237   0.000  0.00  0.00           C+0
HETATM   56  C   UNK     0       4.783   7.993   0.000  0.00  0.00           C+0
HETATM   57  C   UNK     0      -4.588  -2.521   0.000  0.00  0.00           C+0
HETATM   58  C   UNK     0      -5.552 -10.613   0.000  0.00  0.00           C+0
HETATM   59  C   UNK     0       1.293   1.319   0.000  0.00  0.00           C+0
HETATM   60  C   UNK     0      10.763   6.514   0.000  0.00  0.00           C+0
HETATM   61  C   UNK     0       0.012   5.758   0.000  0.00  0.00           C+0
HETATM   62  C   UNK     0       6.278   7.623   0.000  0.00  0.00           C+0
HETATM   63  C   UNK     0      -3.725  -3.796   0.000  0.00  0.00           C+0
HETATM   64  C   UNK     0      -4.016 -10.503   0.000  0.00  0.00           C+0
HETATM   65  C   UNK     0       2.788   0.949   0.000  0.00  0.00           C+0
HETATM   66  C   UNK     0      11.190   5.034   0.000  0.00  0.00           C+0
HETATM   67  C   UNK     0       1.507   5.388   0.000  0.00  0.00           C+0
HETATM   68  C   UNK     0       6.705   6.144   0.000  0.00  0.00           C+0
HETATM   69  C   UNK     0      -3.534  -6.457   0.000  0.00  0.00           C+0
HETATM   70  C   UNK     0      -1.807  -9.007   0.000  0.00  0.00           C+0
HETATM   71  C   UNK     0       5.351   1.689   0.000  0.00  0.00           C+0
HETATM   72  C   UNK     0      10.549   2.445   0.000  0.00  0.00           C+0
HETATM   73  C   UNK     0      13.035 -14.489   0.000  0.00  0.00           C+0
HETATM   74  C   UNK     0      11.729  -9.029   0.000  0.00  0.00           C+0
HETATM   75  C   UNK     0       7.486 -14.295   0.000  0.00  0.00           C+0
HETATM   76  C   UNK     0       7.353 -12.447   0.000  0.00  0.00           C+0
HETATM   77  C   UNK     0       4.819  -4.521   0.000  0.00  0.00           C+0
HETATM   78  C   UNK     0      10.290  -5.465   0.000  0.00  0.00           C+0
HETATM   79  C   UNK     0      -4.397  -5.182   0.000  0.00  0.00           C+0
HETATM   80  C   UNK     0      -3.343  -9.117   0.000  0.00  0.00           C+0
HETATM   81  C   UNK     0       3.856   2.059   0.000  0.00  0.00           C+0
HETATM   82  C   UNK     0      10.122   3.924   0.000  0.00  0.00           C+0
HETATM   83  C   UNK     0      11.929 -15.561   0.000  0.00  0.00           C+0
HETATM   84  C   UNK     0       8.592 -13.224   0.000  0.00  0.00           C+0
HETATM   85  C   UNK     0       7.511 -10.916   0.000  0.00  0.00           C+0
HETATM   86  C   UNK     0      11.570 -10.561   0.000  0.00  0.00           C+0
HETATM   87  C   UNK     0       3.283  -4.631   0.000  0.00  0.00           C+0
HETATM   88  C   UNK     0       9.427  -4.190   0.000  0.00  0.00           C+0
HETATM   89  C   UNK     0      -2.492  -5.919   0.000  0.00  0.00           C+0
HETATM   90  C   UNK     0       5.778   0.209   0.000  0.00  0.00           C+0
HETATM   91  C   UNK     0       1.934   3.908   0.000  0.00  0.00           C+0
HETATM   92  C   UNK     0       8.200   5.774   0.000  0.00  0.00           C+0
HETATM   93  C   UNK     0      -0.641  -8.050   0.000  0.00  0.00           C+0
HETATM   94  C   UNK     0       9.482   1.335   0.000  0.00  0.00           C+0
HETATM   95  C   UNK     0       0.211  -4.851   0.000  0.00  0.00           C+0
HETATM   96  C   UNK     0       7.700  -1.640   0.000  0.00  0.00           C+0
HETATM   97  C   UNK     0      10.448 -15.139   0.000  0.00  0.00           C+0
HETATM   98  C   UNK     0      10.165 -11.190   0.000  0.00  0.00           C+0
HETATM   99  C   UNK     0       2.610  -6.016   0.000  0.00  0.00           C+0
HETATM  100  C   UNK     0      10.073 -13.646   0.000  0.00  0.00           C+0
HETATM  101  C   UNK     0       8.917 -10.287   0.000  0.00  0.00           C+0
HETATM  102  C   UNK     0      10.100  -2.805   0.000  0.00  0.00           C+0
HETATM  103  C   UNK     0       1.074  -6.126   0.000  0.00  0.00           C+0
HETATM  104  C   UNK     0       9.236  -1.530   0.000  0.00  0.00           C+0
HETATM  105  C   UNK     0       7.027  -3.025   0.000  0.00  0.00           C+0
HETATM  106  C   UNK     0       0.883  -3.466   0.000  0.00  0.00           C+0
HETATM  107  C   UNK     0      11.587  -7.054   0.000  0.00  0.00           C+0
HETATM  108  C   UNK     0      14.196 -12.885   0.000  0.00  0.00           C+0
HETATM  109  C   UNK     0      10.481  -8.126   0.000  0.00  0.00           C+0
HETATM  110  C   UNK     0      12.660 -12.996   0.000  0.00  0.00           C+0
HETATM  111  N   UNK     0      -1.325  -4.961   0.000  0.00  0.00           N+0
HETATM  112  N   UNK     0       7.273  -0.160   0.000  0.00  0.00           N+0
HETATM  113  O   UNK     0       7.861 -15.789   0.000  0.00  0.00           O+0
HETATM  114  O   UNK     0       5.947 -13.076   0.000  0.00  0.00           O+0
HETATM  115  O   UNK     0      -5.933  -5.292   0.000  0.00  0.00           O+0
HETATM  116  O   UNK     0      -4.207  -7.842   0.000  0.00  0.00           O+0
HETATM  117  O   UNK     0      12.304 -17.055   0.000  0.00  0.00           O+0
HETATM  118  O   UNK     0       8.216 -11.730   0.000  0.00  0.00           O+0
HETATM  119  O   UNK     0       6.264 -10.013   0.000  0.00  0.00           O+0
HETATM  120  O   UNK     0      -1.134  -7.622   0.000  0.00  0.00           O-1
HETATM  121  O   UNK     0       4.710  -0.900   0.000  0.00  0.00           O-1
HETATM  122  O   UNK     0       0.866   2.799   0.000  0.00  0.00           O+0
HETATM  123  O   UNK     0       9.268   6.884   0.000  0.00  0.00           O+0
HETATM  124  O   UNK     0      -1.998  -6.347   0.000  0.00  0.00           O+0
HETATM  125  O   UNK     0       7.987   1.705   0.000  0.00  0.00           O+0
HETATM  126  O   UNK     0       9.342 -16.211   0.000  0.00  0.00           O+0
HETATM  127  O   UNK     0      10.006 -12.722   0.000  0.00  0.00           O+0
HETATM  128  O   UNK     0       3.473  -7.291   0.000  0.00  0.00           O+0
HETATM  129  O   UNK     0      13.068  -7.476   0.000  0.00  0.00           O+0
HETATM  130  O   UNK     0      11.212  -5.561   0.000  0.00  0.00           O-1
HETATM  131  O   UNK     0      14.868 -11.500   0.000  0.00  0.00           O+0
HETATM  132  O   UNK     0      15.059 -14.161   0.000  0.00  0.00           O-1
HETATM  133  O   UNK     0      11.224  -4.833   0.000  0.00  0.00           O-1
HETATM  134  O   UNK     0      13.774  -3.107   0.000  0.00  0.00           O-1
HETATM  135  O   UNK     0      13.363  -5.245   0.000  0.00  0.00           O+0
HETATM  136  O   UNK     0      -1.406  -3.837   0.000  0.00  0.00           O+0
HETATM  137  O   UNK     0      -1.626  -0.765   0.000  0.00  0.00           O+0
HETATM  138  O   UNK     0      -3.052  -2.411   0.000  0.00  0.00           O+0
HETATM  139  O   UNK     0       5.491  -3.135   0.000  0.00  0.00           O+0
HETATM  140  O   UNK     0       9.618  -6.851   0.000  0.00  0.00           O+0
HETATM  141  O   UNK     0       3.429   3.538   0.000  0.00  0.00           O+0
HETATM  142  O   UNK     0       8.627   4.294   0.000  0.00  0.00           O+0
HETATM  143  O   UNK     0       2.419  -3.356   0.000  0.00  0.00           O+0
HETATM  144  O   UNK     0       7.891  -4.300   0.000  0.00  0.00           O+0
HETATM  145  O   UNK     0       0.401  -7.512   0.000  0.00  0.00           O+0
HETATM  146  O   UNK     0       9.909  -0.144   0.000  0.00  0.00           O+0
HETATM  147  O   UNK     0      12.818 -11.464   0.000  0.00  0.00           O+0
HETATM  148  O   UNK     0       9.075  -8.755   0.000  0.00  0.00           O+0
HETATM  149  O   UNK     0      11.179 -12.574   0.000  0.00  0.00           O+0
HETATM  150  O   UNK     0      11.636  -2.695   0.000  0.00  0.00           O+0
HETATM  151  O   UNK     0       0.020  -2.191   0.000  0.00  0.00           O+0
HETATM  152  P   UNK     0      12.499  -3.970   0.000  0.00  0.00           P+0
HETATM  153  P   UNK     0      -1.516  -2.301   0.000  0.00  0.00           P+0
HETATM  154  H   UNK     0      -2.861  -5.072   0.000  0.00  0.00           H+0
HETATM  155  H   UNK     0      -2.480 -10.393   0.000  0.00  0.00           H+0
HETATM  156  H   UNK     0       4.283   0.579   0.000  0.00  0.00           H+0
HETATM  157  H   UNK     0      11.617   3.554   0.000  0.00  0.00           H+0
HETATM  158  H   UNK     0      10.823 -16.633   0.000  0.00  0.00           H+0
HETATM  159  H   UNK     0       8.967 -14.717   0.000  0.00  0.00           H+0
HETATM  160  H   UNK     0       7.670  -9.384   0.000  0.00  0.00           H+0
HETATM  161  H   UNK     0      11.412 -12.093   0.000  0.00  0.00           H+0
HETATM  162  H   UNK     0       4.146  -5.906   0.000  0.00  0.00           H+0
HETATM  163  H   UNK     0      10.963  -4.080   0.000  0.00  0.00           H+0
HETATM  164  H   UNK     0      -0.462  -6.237   0.000  0.00  0.00           H+0
HETATM  165  H   UNK     0       6.166  -1.508   0.000  0.00  0.00           H+0
HETATM  166  H   UNK     0      11.554 -14.067   0.000  0.00  0.00           H+0
HETATM  167  H   UNK     0       8.759 -11.819   0.000  0.00  0.00           H+0
HETATM  168  H   UNK     0       1.937  -7.402   0.000  0.00  0.00           H+0
HETATM  169  H   UNK     0       9.101 -12.450   0.000  0.00  0.00           H+0
HETATM  170  H   UNK     0      10.323  -9.658   0.000  0.00  0.00           H+0
HETATM  171  H   UNK     0      10.772  -1.420   0.000  0.00  0.00           H+0
HETATM  172  H   UNK     0       1.747  -4.741   0.000  0.00  0.00           H+0
HETATM  173  H   UNK     0       8.564  -2.915   0.000  0.00  0.00           H+0
HETATM  174  H   UNK     0       6.355  -4.411   0.000  0.00  0.00           H+0
HETATM  175  H   UNK     0      -0.653  -3.576   0.000  0.00  0.00           H+0
CONECT    1    7                                                            
CONECT    2    8                                                            
CONECT    3    9                                                            
CONECT    4   10                                                            
CONECT    5   11                                                            
CONECT    6   12                                                            
CONECT    7    1   13                                                       
CONECT    8    2   14                                                       
CONECT    9    3   15                                                       
CONECT   10    4   16                                                       
CONECT   11    5   17                                                       
CONECT   12    6   18                                                       
CONECT   13    7   19                                                       
CONECT   14    8   20                                                       
CONECT   15    9   21                                                       
CONECT   16   10   22                                                       
CONECT   17   11   23                                                       
CONECT   18   12   24                                                       
CONECT   19   13   25                                                       
CONECT   20   14   26                                                       
CONECT   21   15   27                                                       
CONECT   22   16   28                                                       
CONECT   23   17   29                                                       
CONECT   24   18   30                                                       
CONECT   25   19   31                                                       
CONECT   26   20   32                                                       
CONECT   27   21   33                                                       
CONECT   28   22   34                                                       
CONECT   29   23   35                                                       
CONECT   30   24   36                                                       
CONECT   31   25   37                                                       
CONECT   32   26   39                                                       
CONECT   33   27   40                                                       
CONECT   34   28   41                                                       
CONECT   35   29   42                                                       
CONECT   36   30   43                                                       
CONECT   37   31   38                                                       
CONECT   38   37   44                                                       
CONECT   39   32   45                                                       
CONECT   40   33   46                                                       
CONECT   41   34   47                                                       
CONECT   42   35   48                                                       
CONECT   43   36   49                                                       
CONECT   44   38   50                                                       
CONECT   45   39   51                                                       
CONECT   46   40   52                                                       
CONECT   47   41   53                                                       
CONECT   48   42   54                                                       
CONECT   49   43   55                                                       
CONECT   50   44   56                                                       
CONECT   51   45   57                                                       
CONECT   52   46   58                                                       
CONECT   53   47   59                                                       
CONECT   54   48   60                                                       
CONECT   55   49   61                                                       
CONECT   56   50   62                                                       
CONECT   57   51   63                                                       
CONECT   58   52   64                                                       
CONECT   59   53   65                                                       
CONECT   60   54   66                                                       
CONECT   61   55   67                                                       
CONECT   62   56   68                                                       
CONECT   63   57   79                                                       
CONECT   64   58   80                                                       
CONECT   65   59   81                                                       
CONECT   66   60   82                                                       
CONECT   67   61   91                                                       
CONECT   68   62   92                                                       
CONECT   69   79   89                                                       
CONECT   70   80   93                                                       
CONECT   71   81   90                                                       
CONECT   72   82   94                                                       
CONECT   73   83  110                                                       
CONECT   74   86  109                                                       
CONECT   75   84  113                                                       
CONECT   76   85  114                                                       
CONECT   77   87  139                                                       
CONECT   78   88  140                                                       
CONECT   79   63   69  115  154                                             
CONECT   80   64   70  116  155                                             
CONECT   81   65   71  141  156                                             
CONECT   82   66   72  142  157                                             
CONECT   83   73   97  117  158                                             
CONECT   84   75  100  118  159                                             
CONECT   85   76  101  119  160                                             
CONECT   86   74   98  147  161                                             
CONECT   87   77   99  143  162                                             
CONECT   88   78  102  144  163                                             
CONECT   89   69  111  120                                                  
CONECT   90   71  112  121                                                  
CONECT   91   67  122  141                                                  
CONECT   92   68  123  142                                                  
CONECT   93   70  124  145                                                  
CONECT   94   72  125  146                                                  
CONECT   95  103  106  111  164                                             
CONECT   96  104  105  112  165                                             
CONECT   97   83  100  126  166                                             
CONECT   98   86  101  127  167                                             
CONECT   99   87  103  128  168                                             
CONECT  100   84   97  149  169                                             
CONECT  101   85   98  148  170                                             
CONECT  102   88  104  150  171                                             
CONECT  103   95   99  145  172                                             
CONECT  104   96  102  146  173                                             
CONECT  105   96  139  144  174                                             
CONECT  106   95  143  151  175                                             
CONECT  107  109  129  130                                                  
CONECT  108  110  131  132                                                  
CONECT  109   74  107  140  148                                             
CONECT  110   73  108  147  149                                             
CONECT  111   89   95                                                       
CONECT  112   90   96                                                       
CONECT  113   75                                                            
CONECT  114   76                                                            
CONECT  115   79                                                            
CONECT  116   80                                                            
CONECT  117   83                                                            
CONECT  118   84                                                            
CONECT  119   85                                                            
CONECT  120   89                                                            
CONECT  121   90                                                            
CONECT  122   91                                                            
CONECT  123   92                                                            
CONECT  124   93                                                            
CONECT  125   94                                                            
CONECT  126   97                                                            
CONECT  127   98                                                            
CONECT  128   99                                                            
CONECT  129  107                                                            
CONECT  130  107                                                            
CONECT  131  108                                                            
CONECT  132  108                                                            
CONECT  133  152                                                            
CONECT  134  152                                                            
CONECT  135  152                                                            
CONECT  136  153                                                            
CONECT  137  153                                                            
CONECT  138  153                                                            
CONECT  139   77  105                                                       
CONECT  140   78  109                                                       
CONECT  141   81   91                                                       
CONECT  142   82   92                                                       
CONECT  143   87  106                                                       
CONECT  144   88  105                                                       
CONECT  145   93  103                                                       
CONECT  146   94  104                                                       
CONECT  147   86  110                                                       
CONECT  148  101  109                                                       
CONECT  149  100  110                                                       
CONECT  150  102  152                                                       
CONECT  151  106  153                                                       
CONECT  152  133  134  135  150                                             
CONECT  153  136  137  138  151                                             
CONECT  154   79                                                            
CONECT  155   80                                                            
CONECT  156   81                                                            
CONECT  157   82                                                            
CONECT  158   83                                                            
CONECT  159   84                                                            
CONECT  160   85                                                            
CONECT  161   86                                                            
CONECT  162   87                                                            
CONECT  163   88                                                            
CONECT  164   95                                                            
CONECT  165   96                                                            
CONECT  166   97                                                            
CONECT  167   98                                                            
CONECT  168   99                                                            
CONECT  169  100                                                            
CONECT  170  101                                                            
CONECT  171  102                                                            
CONECT  172  103                                                            
CONECT  173  104                                                            
CONECT  174  105                                                            
CONECT  175  106                                                            
MASTER        0    0    0    0    0    0    0    0  175    0  356    0
END

Synonyms

Value	Source
alpha-Kdo-(2->4)-alpha-kdo-(2->6)-lipid a	ChEBI
a-Kdo-(2->4)-a-kdo-(2->6)-lipid a	Generator
Α-kdo-(2->4)-α-kdo-(2->6)-lipid a	Generator

Molecular Formula

C₁₁₀H₁₉₆N₂O₃₉P₂

Average Mass

2232.704

Monoisotopic Mass

2231.292339975

IUPAC Name

(2R,4R,5R,6R)-2-{[(2R,4R,5R,6R)-2-carboxylato-6-[(1R)-1,2-dihydroxyethyl]-2-{[(2R,3S,4R,5R,6R)-5-{[(3R)-3-(dodecanoyloxy)-1-oxidotetradecylidene]amino}-6-{[(2R,3S,4R,5R,6R)-3-hydroxy-5-{[(3R)-3-hydroxy-1-oxidotetradecylidene]amino}-4-{[(3R)-3-hydroxytetradecanoyl]oxy}-6-(phosphonooxy)oxan-2-yl]methoxy}-3-(phosphonatooxy)-4-{[(3R)-3-(tetradecanoyloxy)tetradecanoyl]oxy}oxan-2-yl]methoxy}-5-hydroxyoxan-4-yl]oxy}-6-[(1R)-1,2-dihydroxyethyl]-4,5-dihydroxyoxane-2-carboxylate

Traditional Name

CAS Registry Number

Not Available

SMILES

[H][C@@](O)(CCCCCCCCCCC)CC(=O)O[C@@]1([H])[C@]([H])(O)[C@@]([H])(CO[C@]2([H])O[C@]([H])(CO[C@@]3(C[C@@]([H])(O[C@@]4(C[C@@]([H])(O)[C@@]([H])(O)[C@]([H])(O4)[C@]([H])(O)CO)C([O-])=O)[C@@]([H])(O)[C@]([H])(O3)[C@]([H])(O)CO)C([O-])=O)[C@@]([H])(OP([O-])([O-])=O)[C@]([H])(OC(=O)C[C@@]([H])(CCCCCCCCCCC)OC(=O)CCCCCCCCCCCCC)[C@@]2([H])N=C([O-])C[C@@]([H])(CCCCCCCCCCC)OC(=O)CCCCCCCCCCC)O[C@]([H])(OP(O)(O)=O)[C@]1([H])N=C([O-])C[C@]([H])(O)CCCCCCCCCCC

InChI Identifier

InChI=1S/C110H202N2O39P2/c1-7-13-19-25-31-37-38-44-50-56-62-68-92(123)142-82(66-60-54-48-42-35-29-23-17-11-5)72-94(125)146-104-96(112-90(121)71-81(65-59-53-47-41-34-28-22-16-10-4)141-91(122)67-61-55-49-43-36-30-24-18-12-6)105(144-88(102(104)150-152(133,134)135)78-140-109(107(129)130)74-86(98(127)101(148-109)85(119)76-114)147-110(108(131)132)73-83(117)97(126)100(149-110)84(118)75-113)139-77-87-99(128)103(145-93(124)70-80(116)64-58-52-46-40-33-27-21-15-9-3)95(106(143-87)151-153(136,137)138)111-89(120)69-79(115)63-57-51-45-39-32-26-20-14-8-2/h79-88,95-106,113-119,126-128H,7-78H2,1-6H3,(H,111,120)(H,112,121)(H,129,130)(H,131,132)(H2,133,134,135)(H2,136,137,138)/p-6/t79-,80-,81-,82-,83-,84-,85-,86-,87-,88-,95-,96-,97-,98-,99-,100-,101-,102-,103-,104-,105-,106-,109-,110-/m1/s1

InChI Key

DIXUKJUHGLIZGU-OIPVZEHTSA-H

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as acylaminosugars. These are organic compounds containing a sugar linked to a chain through N-acyl group.

Kingdom

Organic compounds

Super Class

Organic oxygen compounds

Class

Organooxygen compounds

Sub Class

Carbohydrates and carbohydrate conjugates

Direct Parent

Acylaminosugars

Alternative Parents

Substituents

Oligosaccharide phosphate
Oligosaccharide
Hexacarboxylic acid or derivatives
Acylaminosugar
Saccharolipid
Hexose phosphate
N-acyl-alpha-hexosamine
C-glucuronide
C-glycosyl compound
Glycosyl compound
O-glycosyl compound
Beta-hydroxy acid
Ketal
Fatty acid ester
Fatty amide
Fatty acyl
Hydroxy acid
N-acyl-amine
Alkyl phosphate
Pyran
Organic phosphoric acid derivative
Oxane
Phosphoric acid ester
Carboxamide group
Secondary alcohol
Secondary carboxylic acid amide
Carboxylic acid ester
Carboxylic acid derivative
Organoheterocyclic compound
Carboxylic acid
Oxacycle
Acetal
Primary alcohol
Organopnictogen compound
Alcohol
Organic oxide
Carbonyl group
Organonitrogen compound
Hydrocarbon derivative
Organic nitrogen compound
Organic anion
Aliphatic heteromonocyclic compound

Molecular Framework

Aliphatic heteromonocyclic compounds

External Descriptors

dicarboxylic acid dianion (CHEBI:58540 )
carbohydrate acid derivative anion (CHEBI:58540 )
anionic phospholipid (CHEBI:58540 )

Functional Ontology

Not Available

Physical Properties

State

Expected Solid

Predicted Properties

Property	Value	Source
Water Solubility	0.026 g/L	ALOGPS
logP	5.01	ALOGPS
logP	22.64	ChemAxon
logS	-5	ALOGPS
pKa (Strongest Acidic)	0.55	ChemAxon
Physiological Charge	-6	ChemAxon
Hydrogen Acceptor Count	35	ChemAxon
Hydrogen Donor Count	12	ChemAxon
Polar Surface Area	662.39 Å²	ChemAxon
Rotatable Bond Count	98	ChemAxon
Refractivity	605.17 m³·mol⁻¹	ChemAxon
Polarizability	249.52 Å³	ChemAxon
Number of Rings	4	ChemAxon
Bioavailability	No	ChemAxon
Rule of Five	No	ChemAxon
Ghose Filter	No	ChemAxon
Veber's Rule	No	ChemAxon
MDDR-like Rule	Yes	ChemAxon

Spectra

Spectrum Type	Description	Splash Key	Deposition Date	View
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Positive	splash10-000x-1290000000-11ae518f9b6e3d1febec	2015-09-16	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Positive	splash10-00dl-2290000000-1fe35c45b114339ac9d3	2015-09-16	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Positive	splash10-052f-8961100000-83ffd298ca91aa9bb219	2015-09-16	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Negative	splash10-001r-3190000000-ca0d72bf7d698f820ffa	2015-09-16	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Negative	splash10-0umi-9742000000-c7f89f307f213742d992	2015-09-16	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Negative	splash10-06vi-9320000000-fe409eb62d6fb5c8e661	2015-09-16	View Spectrum

Biological Properties

Cellular Locations

Not Available

Biospecimen Locations

Not Available

Tissue Locations

Not Available

Associated OMIM IDs

114500 (Colorectal cancer)
610247 (Eosinophilic esophagitis)

Human Proteins and Enzymes

Protein ID	Protein Name	Protein Type	Uniprot ID	Species

Human Pathways

Pathways

Name	SMPDB/PathBank

Metabolic Reactions

Reaction ID	Precursor	Product	Enzyme	Reaction Type	Data Source	Reference
MMDBr0016132	(KDO)2-lipid A	(Kdo)2-lipid A 1-diphosphate	Lipid A 1-diphosphate synthase	Synthesis	RHEA	34755880
MMDBr0018387	Lauroyl-KDO2-lipid IV(A)	(KDO)2-lipid A	Lipid A biosynthesis myristoyltransferase	Synthesis	PathBank	31602464
MMDBr0018388	(KDO)2-lipid A	Hydrogen Ion	Lipopolysaccharide heptosyltransferase 1		PathBank	31602464
MMDBr0019255	4-Amino-4-deoxy-alpha-L-arabinopyranosyl di-trans,octa-cis-undecaprenyl phosphate	L-Ara4N-modified KDO2-Lipid A	Undecaprenyl phosphate-alpha-4-amino-4-deoxy-L-arabinose arabinosyl transferase	Transfer of the L-Ara4N moiety	PathBank	31602464
MMDBr0024788	(KDO)2-lipid A	7-O-[2-aminoethoxy(hydroxy)phosphoryl]-alpha-Kdo-(2->4)-alpha-Kdo-(2->6)-lipid A	Kdo(2)-lipid A phosphoethanolamine 7''-transferase	Transfer of Kdo(2)-lipid A phosphoethanolamine	RHEA	34755880
MMDBr0024836	KDO(2)-lipid IV(A) with laurate	(KDO)2-lipid A	Lipid A biosynthesis myristoyltransferase 2	Synthesis	RHEA	34755880

Health Effects and Bioactivity

Health Outcome/Bioactivity	Metabolite Response/Effect	Evidence Type	Host and Biospecimen	Data Source	Reference

Microbial Sources

Superkingdom/Kingdom	Phylum	Total species	Hosts and Body Sites	Microbial Links
Bacteria	Proteobacteria	1	Human ; Human feces; Human feces; pleural fluid plaque; bal; Human stool	Unknown

Exposure Sources

Source Type	Source Sub-type	Species	Data Source	Reference

Host Biospecimen and Location

Host and Biospecimen	Status	Mean	Std	Min	Max	Units	Age	Sex	Health Condition	Data Source	Reference

External Links

HMDB ID

Not Available

DrugBank ID

Not Available

Phenol Explorer Compound ID

Not Available

FooDB ID

Not Available

KNApSAcK ID

Not Available

Chemspider ID

Not Available

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

25244473

PDB ID

Not Available

ChEBI ID

58540

Food Biomarker Ontology

Not Available

References

Synthesis Reference

Not Available

General References

Wishart DS, Li C, Marcu A, Badran H, Pon A, Budinski Z, Patron J, Lipton D, Cao X, Oler E, Li K, Paccoud M, Hong C, Guo AC, Chan C, Wei W, Ramirez-Gaona M: PathBank: a comprehensive pathway database for model organisms. Nucleic Acids Res. 2020 Jan 8;48(D1):D470-D478. doi: 10.1093/nar/gkz861. [PubMed:31602464 ]
Bansal P, Morgat A, Axelsen KB, Muthukrishnan V, Coudert E, Aimo L, Hyka-Nouspikel N, Gasteiger E, Kerhornou A, Neto TB, Pozzato M, Blatter MC, Ignatchenko A, Redaschi N, Bridge A: Rhea, the reaction knowledgebase in 2022. Nucleic Acids Res. 2022 Jan 7;50(D1):D693-D700. doi: 10.1093/nar/gkab1016. [PubMed:34755880 ]

Showing metabocard for (KDO)2-lipid A (MMDBc0032104)

MOL for #<Metabolite:0x00007fa4f56ee2f8>

3D MOL for #<Metabolite:0x00007fa4f56ee2f8>

3D SDF for #<Metabolite:0x00007fa4f56ee2f8>

3D-SDF for #<Metabolite:0x00007fa4f56ee2f8>

PDB for #<Metabolite:0x00007fa4f56ee2f8>

3D PDB for #<Metabolite:0x00007fa4f56ee2f8>

SMILES for #<Metabolite:0x00007fa4f56ee2f8>

INCHI for #<Metabolite:0x00007fa4f56ee2f8>

Structure for #<Metabolite:0x00007fa4f56ee2f8>

3D Structure for #<Metabolite:0x00007fa4f56ee2f8>