MiMeDB: Showing metabocard for Adenosyl cobinamide (MMDBc0029849)

Record Information

Version

1.0

Status

Detected and Quantified

Creation Date

2021-11-17 23:44:09 UTC

Update Date

2022-08-31 17:19:27 UTC

Metabolite ID

MMDBc0029849

Metabolite Identification

Common Name

Adenosyl cobinamide

Description

Adenosyl cobinamide is an intermediate in Porphyrin and chlorophyll metabolism. It is the third to last step in the synthesis of vitamin B12 coenzyme and is converted from adenosyl cobyrinate hexaamide via the enzyme cobalamin biosynthetic protein CobC. It is then converted to adenosyl cobinamide phosphate via the enzyme adenosylcobinamide kinase / adenosylcobinamide-phosphate guanylyltransferase [EC:2.7.1.156 and EC 2.7.7.62].

Structure

MOL SDF PDB SMILES InChI


  Mrv1652305221921292D          

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M  CHG  2  49  -1  86   3
M  RAD  1  68   2
M  END


  Mrv1652305221921292D          

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   -0.2193   -4.9987    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.0423   -1.2349    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -4.5419   -0.7444    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.2828   -4.0623    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.1613    2.8586    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    8.4776   -2.0361    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   12.3982    0.5684    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    9.6997    0.9809    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    9.1451   -1.5511    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   10.9693    1.3934    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    9.9297   -1.8061    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   10.4146   -1.1386    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   11.6837    1.8059    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   10.9693    0.5684    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    9.9297   -0.4712    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   11.6837    2.6309    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   12.3982    1.3934    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   11.6837    0.1559    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   10.1846    1.6483    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   10.1846    0.3134    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   10.1846   -2.5907    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   11.2396   -1.1386    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    9.1451   -0.7261    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -6.6141    0.4797    0.0000 Co  0  1  0  0  0  0  0  0  0  0  0  0
    5.1031    3.8555    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.9223    1.4651    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.7480    1.5466    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1473   -2.1292    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.8268   -1.0302    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.4565   -0.2866    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
 13 10  1  0  0  0  0
 14 11  1  0  0  0  0
 15 12  1  0  0  0  0
 17 16  1  0  0  0  0
 23  1  1  0  0  0  0
 23 22  1  0  0  0  0
 24  2  1  4  0  0  0
 25  3  1  4  0  0  0
 26 10  1  6  0  0  0
 27 11  1  1  0  0  0
 28 12  1  6  0  0  0
 29 18  1  1  0  0  0
 30 19  2  0  0  0  0
 30 26  1  0  0  0  0
 19 31  1  4  0  0  0
 32 13  1  0  0  0  0
 33 14  1  0  0  0  0
 34 15  1  0  0  0  0
 35 18  1  0  0  0  0
 36 20  1  0  0  0  0
 37 21  1  0  0  0  0
 38 16  1  0  0  0  0
 39 24  2  0  0  0  0
 39 27  1  0  0  0  0
 40 25  2  0  0  0  0
 40 28  1  0  0  0  0
 41 24  1  0  0  0  0
 42 25  1  0  0  0  0
 43 29  1  0  0  0  0
 44  4  1  0  0  0  0
 44  5  1  0  0  0  0
 44 27  1  0  0  0  0
 44 31  1  0  0  0  0
 45  6  1  1  0  0  0
 45 17  1  6  0  0  0
 45 29  1  0  0  0  0
 45 41  1  0  0  0  0
 46  7  1  6  0  0  0
 46 20  1  1  0  0  0
 46 26  1  0  0  0  0
 46 42  1  0  0  0  0
 47  8  1  6  0  0  0
 47 21  1  1  0  0  0
 47 28  1  0  0  0  0
 48  9  1  6  0  0  0
 48 43  1  0  0  0  0
 48 47  1  0  0  0  0
 49 32  1  0  0  0  0
 50 33  2  0  0  0  0
 51 34  2  0  0  0  0
 52 35  2  0  0  0  0
 53 36  2  0  0  0  0
 54 37  2  0  0  0  0
 55 22  1  4  0  0  0
 55 38  2  0  0  0  0
 56 30  1  0  0  0  0
 56 42  2  0  0  0  0
 57 31  2  0  0  0  0
 57 39  1  0  0  0  0
 58 41  2  0  0  0  0
 58 43  1  0  0  0  0
 59 40  1  0  0  0  0
 59 48  1  0  0  0  0
 23 60  1  6  0  0  0
 61 32  2  0  0  0  0
 62 33  1  0  0  0  0
 63 34  1  0  0  0  0
 64 35  1  0  0  0  0
 65 36  1  0  0  0  0
 66 37  1  0  0  0  0
 67 38  1  0  0  0  0
 71 68  1  0  0  0  0
 73 71  1  0  0  0  0
 74 73  1  0  0  0  0
 75 72  2  0  0  0  0
 76 72  1  0  0  0  0
 77 74  1  0  0  0  0
 78 75  1  0  0  0  0
 79 69  2  0  0  0  0
 79 75  1  0  0  0  0
 80 69  1  0  0  0  0
 80 76  2  0  0  0  0
 81 70  2  0  0  0  0
 81 72  1  0  0  0  0
 82 70  1  0  0  0  0
 82 76  1  0  0  0  0
 82 77  1  0  0  0  0
 83 73  1  0  0  0  0
 84 74  1  0  0  0  0
 85 71  1  0  0  0  0
 85 77  1  0  0  0  0
 23 87  1  6  0  0  0
 26 88  1  1  0  0  0
 27 89  1  6  0  0  0
 28 90  1  1  0  0  0
 29 91  1  6  0  0  0
 43 92  1  1  0  0  0
M  CHG  2  49  -1  86   3
M  RAD  1  68   2
M  END
> <DATABASE_ID>
MMDBc0029849

> <DATABASE_NAME>
MIME

> <SMILES>
[Co+3].[CH2]C1OC(C(O)C1O)N1C=NC2=C(N)N=CN=C12.[H][C@](C)(O)CN=C(O)CC[C@@]1(C)C2=N[C@]([H])([C@]1([H])CC(O)=N)[C@]1(C)NC(=C(C)C3=NC(=CC4=NC(=C2C)[C@@]([H])(CCC(O)=N)C4(C)C)[C@@]([H])(CCC([NH-])=O)[C@]3(C)CC(O)=N)[C@@]([H])(CCC(O)=N)[C@]1(C)CC(O)=N

> <INCHI_IDENTIFIER>
InChI=1S/C48H73N11O8.C10H12N5O3.Co/c1-23(60)22-55-38(67)16-17-45(6)29(18-35(52)64)43-48(9)47(8,21-37(54)66)28(12-15-34(51)63)40(59-48)25(3)42-46(7,20-36(53)65)26(10-13-32(49)61)30(56-42)19-31-44(4,5)27(11-14-33(50)62)39(57-31)24(2)41(45)58-43;1-4-6(16)7(17)10(18-4)15-3-14-5-8(11)12-2-13-9(5)15;/h19,23,26-29,43,60H,10-18,20-22H2,1-9H3,(H14,49,50,51,52,53,54,55,56,57,58,59,61,62,63,64,65,66,67);2-4,6-7,10,16-17H,1H2,(H2,11,12,13);/q;;+3/p-1/t23-,26-,27-,28-,29+,43-,45-,46+,47+,48+;;/m1../s1

> <INCHI_KEY>
PAUPKJHCFVPREX-VUCSARQQSA-M

> <FORMULA>
C58H84CoN16O11

> <MOLECULAR_WEIGHT>
1240.3214

> <EXACT_MASS>
1239.583747804

> <JCHEM_ACCEPTOR_COUNT>
19

> <JCHEM_ATOM_COUNT>
170

> <JCHEM_AVERAGE_POLARIZABILITY>
100.6225522169776

> <JCHEM_BIOAVAILABILITY>
0

> <JCHEM_DONOR_COUNT>
14

> <JCHEM_FORMAL_CHARGE>
2

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
cobalt(3+) ion 3-[(1R,2R,3S,4S,8S,9S,14S,18R,19R)-4,14-bis[2-(C-hydroxycarbonimidoyl)ethyl]-3,8,19-tris[(C-hydroxycarbonimidoyl)methyl]-18-(2-{[(2R)-2-hydroxypropyl]-C-hydroxycarbonimidoyl}ethyl)-2,3,6,8,13,13,16,18-octamethyl-20,21,22,23-tetraazapentacyclo[15.2.1.1^{2,5}.1^{7,10}.1^{12,15}]tricosa-5,7(22),10,12(21),15,17(20)-hexaen-9-yl]propan-1-aminide [5-(6-amino-9H-purin-9-yl)-3,4-dihydroxyoxolan-2-yl]methyl

> <ALOGPS_LOGP>
2.73

> <JCHEM_LOGP>
-2.627622796061467

> <ALOGPS_LOGS>
-4.59

> <JCHEM_MDDR_LIKE_RULE>
1

> <JCHEM_NUMBER_OF_RINGS>
8

> <JCHEM_PHYSIOLOGICAL_CHARGE>
3

> <JCHEM_PKA>
5.3627243789326995

> <JCHEM_PKA_STRONGEST_ACIDIC>
4.974569288744145

> <JCHEM_PKA_STRONGEST_BASIC>
9.068846447579347

> <JCHEM_POLAR_SURFACE_AREA>
359.6300000000001

> <JCHEM_REFRACTIVITY>
308.41299999999984

> <JCHEM_ROTATABLE_BOND_COUNT>
21

> <JCHEM_RULE_OF_FIVE>
0

> <ALOGPS_SOLUBILITY>
2.74e-02 g/l

> <JCHEM_TRADITIONAL_IUPAC>
cobalt(3+) ion 3-[(1R,2R,3S,4S,8S,9S,14S,18R,19R)-4,14-bis[2-(C-hydroxycarbonimidoyl)ethyl]-3,8,19-tris(C-hydroxycarbonimidoylmethyl)-18-(2-{[(2R)-2-hydroxypropyl]-C-hydroxycarbonimidoyl}ethyl)-2,3,6,8,13,13,16,18-octamethyl-20,21,22,23-tetraazapentacyclo[15.2.1.1^{2,5}.1^{7,10}.1^{12,15}]tricosa-5,7(22),10,12(21),15,17(20)-hexaen-9-yl]propan-1-aminide [5-(6-aminopurin-9-yl)-3,4-dihydroxyoxolan-2-yl]methyl

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 22-MAY-19   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   22-MAY-19         0                                  
HETATM    1  C   UNK     0      11.051   7.413   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       3.273   4.196   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0      -4.049  -3.222   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0      -1.619   1.318   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0      -3.199   2.641   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       5.656   0.628   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0      -7.122  -0.227   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0       2.459  -3.889   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0       2.601  -2.881   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0      -6.919   2.066   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0       0.680   1.446   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0      -1.323  -5.360   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0      -8.302   1.389   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0      -0.041   0.085   0.000  0.00  0.00           C+0
HETATM   15  C   UNK     0      -0.506  -6.665   0.000  0.00  0.00           C+0
HETATM   16  C   UNK     0       6.275   2.695   0.000  0.00  0.00           C+0
HETATM   17  C   UNK     0       4.751   2.479   0.000  0.00  0.00           C+0
HETATM   18  C   UNK     0       4.981  -1.573   0.000  0.00  0.00           C+0
HETATM   19  C   UNK     0      -3.353   3.533   0.000  0.00  0.00           C+0
HETATM   20  C   UNK     0      -5.851  -1.850   0.000  0.00  0.00           C+0
HETATM   21  C   UNK     0       0.978  -5.323   0.000  0.00  0.00           C+0
HETATM   22  C   UNK     0       8.951   5.768   0.000  0.00  0.00           C+0
HETATM   23  C   UNK     0      10.475   5.984   0.000  0.00  0.00           C+0
HETATM   24  C   UNK     0       2.138   3.155   0.000  0.00  0.00           C+0
HETATM   25  C   UNK     0      -3.155  -1.968   0.000  0.00  0.00           C+0
HETATM   26  C   UNK     0      -5.641   1.206   0.000  0.00  0.00           C+0
HETATM   27  C   UNK     0      -0.138   2.751   0.000  0.00  0.00           C+0
HETATM   28  C   UNK     0      -0.602  -4.000   0.000  0.00  0.00           C+0
HETATM   29  C   UNK     0       3.910  -0.466   0.000  0.00  0.00           C+0
HETATM   30  C   UNK     0      -4.194   1.735   0.000  0.00  0.00           C+0
HETATM   31  C   UNK     0      -2.048   4.350   0.000  0.00  0.00           C+0
HETATM   32  C   UNK     0      -9.580   2.249   0.000  0.00  0.00           C+0
HETATM   33  C   UNK     0      -1.580   0.030   0.000  0.00  0.00           C+0
HETATM   34  C   UNK     0      -1.227  -8.026   0.000  0.00  0.00           C+0
HETATM   35  C   UNK     0       6.475  -1.199   0.000  0.00  0.00           C+0
HETATM   36  C   UNK     0      -7.297  -2.378   0.000  0.00  0.00           C+0
HETATM   37  C   UNK     0       2.339  -6.044   0.000  0.00  0.00           C+0
HETATM   38  C   UNK     0       6.851   4.124   0.000  0.00  0.00           C+0
HETATM   39  C   UNK     0       0.438   4.180   0.000  0.00  0.00           C+0
HETATM   40  C   UNK     0      -1.279  -2.616   0.000  0.00  0.00           C+0
HETATM   41  C   UNK     0       2.815   1.772   0.000  0.00  0.00           C+0
HETATM   42  C   UNK     0      -4.104  -0.756   0.000  0.00  0.00           C+0
HETATM   43  C   UNK     0       2.385  -0.682   0.000  0.00  0.00           C+0
HETATM   44  C   UNK     0      -1.674   2.857   0.000  0.00  0.00           C+0
HETATM   45  C   UNK     0       4.175   1.051   0.000  0.00  0.00           C+0
HETATM   46  C   UNK     0      -5.585  -0.333   0.000  0.00  0.00           C+0
HETATM   47  C   UNK     0       0.923  -3.784   0.000  0.00  0.00           C+0
HETATM   48  C   UNK     0       1.189  -2.267   0.000  0.00  0.00           C+0
HETATM   49  N   UNK     0     -10.963   1.572   0.000  0.00  0.00           N-1
HETATM   50  N   UNK     0      -2.398   1.335   0.000  0.00  0.00           N+0
HETATM   51  N   UNK     0      -2.766  -8.081   0.000  0.00  0.00           N+0
HETATM   52  N   UNK     0       6.897   0.282   0.000  0.00  0.00           N+0
HETATM   53  N   UNK     0      -7.563  -3.895   0.000  0.00  0.00           N+0
HETATM   54  N   UNK     0       3.644  -5.226   0.000  0.00  0.00           N+0
HETATM   55  N   UNK     0       8.375   4.340   0.000  0.00  0.00           N+0
HETATM   56  N   UNK     0      -3.245   0.522   0.000  0.00  0.00           N+0
HETATM   57  N   UNK     0      -0.743   5.168   0.000  0.00  0.00           N+0
HETATM   58  N   UNK     0       1.708   0.701   0.000  0.00  0.00           N+0
HETATM   59  N   UNK     0      -0.172  -1.545   0.000  0.00  0.00           N+0
HETATM   60  O   UNK     0      11.425   4.772   0.000  0.00  0.00           O+0
HETATM   61  O   UNK     0      -9.474   3.785   0.000  0.00  0.00           O+0
HETATM   62  O   UNK     0      -2.302  -1.331   0.000  0.00  0.00           O+0
HETATM   63  O   UNK     0      -0.409  -9.331   0.000  0.00  0.00           O+0
HETATM   64  O   UNK     0       7.546  -2.305   0.000  0.00  0.00           O+0
HETATM   65  O   UNK     0      -8.478  -1.390   0.000  0.00  0.00           O+0
HETATM   66  O   UNK     0       2.395  -7.583   0.000  0.00  0.00           O+0
HETATM   67  O   UNK     0       5.901   5.336   0.000  0.00  0.00           O+0
HETATM   68  C   UNK     0      15.825  -3.801   0.000  0.00  0.00           C+0
HETATM   69  C   UNK     0      23.143   1.061   0.000  0.00  0.00           C+0
HETATM   70  C   UNK     0      18.106   1.831   0.000  0.00  0.00           C+0
HETATM   71  C   UNK     0      17.071  -2.895   0.000  0.00  0.00           C+0
HETATM   72  C   UNK     0      20.476   2.601   0.000  0.00  0.00           C+0
HETATM   73  C   UNK     0      18.535  -3.371   0.000  0.00  0.00           C+0
HETATM   74  C   UNK     0      19.441  -2.125   0.000  0.00  0.00           C+0
HETATM   75  C   UNK     0      21.810   3.371   0.000  0.00  0.00           C+0
HETATM   76  C   UNK     0      20.476   1.061   0.000  0.00  0.00           C+0
HETATM   77  C   UNK     0      18.535  -0.880   0.000  0.00  0.00           C+0
HETATM   78  N   UNK     0      21.810   4.911   0.000  0.00  0.00           N+0
HETATM   79  N   UNK     0      23.143   2.601   0.000  0.00  0.00           N+0
HETATM   80  N   UNK     0      21.810   0.291   0.000  0.00  0.00           N+0
HETATM   81  N   UNK     0      19.011   3.077   0.000  0.00  0.00           N+0
HETATM   82  N   UNK     0      19.011   0.585   0.000  0.00  0.00           N+0
HETATM   83  O   UNK     0      19.011  -4.836   0.000  0.00  0.00           O+0
HETATM   84  O   UNK     0      20.981  -2.125   0.000  0.00  0.00           O+0
HETATM   85  O   UNK     0      17.071  -1.355   0.000  0.00  0.00           O+0
HETATM   86 Co   UNK     0     -12.346   0.895   0.000  0.00  0.00          Co+3
HETATM   87  H   UNK     0       9.526   7.197   0.000  0.00  0.00           H+0
HETATM   88  H   UNK     0      -5.455   2.735   0.000  0.00  0.00           H+0
HETATM   89  H   UNK     0       1.396   2.887   0.000  0.00  0.00           H+0
HETATM   90  H   UNK     0      -2.142  -3.975   0.000  0.00  0.00           H+0
HETATM   91  H   UNK     0       3.410  -1.923   0.000  0.00  0.00           H+0
HETATM   92  H   UNK     0       0.852  -0.535   0.000  0.00  0.00           H+0
CONECT    1   23                                                            
CONECT    2   24                                                            
CONECT    3   25                                                            
CONECT    4   44                                                            
CONECT    5   44                                                            
CONECT    6   45                                                            
CONECT    7   46                                                            
CONECT    8   47                                                            
CONECT    9   48                                                            
CONECT   10   13   26                                                       
CONECT   11   14   27                                                       
CONECT   12   15   28                                                       
CONECT   13   10   32                                                       
CONECT   14   11   33                                                       
CONECT   15   12   34                                                       
CONECT   16   17   38                                                       
CONECT   17   16   45                                                       
CONECT   18   29   35                                                       
CONECT   19   30   31                                                       
CONECT   20   36   46                                                       
CONECT   21   37   47                                                       
CONECT   22   23   55                                                       
CONECT   23    1   22   60   87                                             
CONECT   24    2   39   41                                                  
CONECT   25    3   40   42                                                  
CONECT   26   10   30   46   88                                             
CONECT   27   11   39   44   89                                             
CONECT   28   12   40   47   90                                             
CONECT   29   18   43   45   91                                             
CONECT   30   19   26   56                                                  
CONECT   31   19   44   57                                                  
CONECT   32   13   49   61                                                  
CONECT   33   14   50   62                                                  
CONECT   34   15   51   63                                                  
CONECT   35   18   52   64                                                  
CONECT   36   20   53   65                                                  
CONECT   37   21   54   66                                                  
CONECT   38   16   55   67                                                  
CONECT   39   24   27   57                                                  
CONECT   40   25   28   59                                                  
CONECT   41   24   45   58                                                  
CONECT   42   25   46   56                                                  
CONECT   43   29   48   58   92                                             
CONECT   44    4    5   27   31                                             
CONECT   45    6   17   29   41                                             
CONECT   46    7   20   26   42                                             
CONECT   47    8   21   28   48                                             
CONECT   48    9   43   47   59                                             
CONECT   49   32                                                            
CONECT   50   33                                                            
CONECT   51   34                                                            
CONECT   52   35                                                            
CONECT   53   36                                                            
CONECT   54   37                                                            
CONECT   55   22   38                                                       
CONECT   56   30   42                                                       
CONECT   57   31   39                                                       
CONECT   58   41   43                                                       
CONECT   59   40   48                                                       
CONECT   60   23                                                            
CONECT   61   32                                                            
CONECT   62   33                                                            
CONECT   63   34                                                            
CONECT   64   35                                                            
CONECT   65   36                                                            
CONECT   66   37                                                            
CONECT   67   38                                                            
CONECT   68   71                                                            
CONECT   69   79   80                                                       
CONECT   70   81   82                                                       
CONECT   71   68   73   85                                                  
CONECT   72   75   76   81                                                  
CONECT   73   71   74   83                                                  
CONECT   74   73   77   84                                                  
CONECT   75   72   78   79                                                  
CONECT   76   72   80   82                                                  
CONECT   77   74   82   85                                                  
CONECT   78   75                                                            
CONECT   79   69   75                                                       
CONECT   80   69   76                                                       
CONECT   81   70   72                                                       
CONECT   82   70   76   77                                                  
CONECT   83   73                                                            
CONECT   84   74                                                            
CONECT   85   71   77                                                       
CONECT   87   23                                                            
CONECT   88   26                                                            
CONECT   89   27                                                            
CONECT   90   28                                                            
CONECT   91   29                                                            
CONECT   92   43                                                            
MASTER        0    0    0    0    0    0    0    0   92    0  194    0
END

Synonyms

Value	Source
5'-Deoxy-5'-adenosylcobinamide	HMDB
Adenosylcobinamide	HMDB

Molecular Formula

C₅₈H₈₄CoN₁₆O₁₁

Average Mass

1240.3214

Monoisotopic Mass

1239.583747804

IUPAC Name

cobalt(3+) ion 3-[(1R,2R,3S,4S,8S,9S,14S,18R,19R)-4,14-bis[2-(C-hydroxycarbonimidoyl)ethyl]-3,8,19-tris[(C-hydroxycarbonimidoyl)methyl]-18-(2-{[(2R)-2-hydroxypropyl]-C-hydroxycarbonimidoyl}ethyl)-2,3,6,8,13,13,16,18-octamethyl-20,21,22,23-tetraazapentacyclo[15.2.1.1^{2,5}.1^{7,10}.1^{12,15}]tricosa-5,7(22),10,12(21),15,17(20)-hexaen-9-yl]propan-1-aminide [5-(6-amino-9H-purin-9-yl)-3,4-dihydroxyoxolan-2-yl]methyl

Traditional Name

cobalt(3+) ion 3-[(1R,2R,3S,4S,8S,9S,14S,18R,19R)-4,14-bis[2-(C-hydroxycarbonimidoyl)ethyl]-3,8,19-tris(C-hydroxycarbonimidoylmethyl)-18-(2-{[(2R)-2-hydroxypropyl]-C-hydroxycarbonimidoyl}ethyl)-2,3,6,8,13,13,16,18-octamethyl-20,21,22,23-tetraazapentacyclo[15.2.1.1^{2,5}.1^{7,10}.1^{12,15}]tricosa-5,7(22),10,12(21),15,17(20)-hexaen-9-yl]propan-1-aminide [5-(6-aminopurin-9-yl)-3,4-dihydroxyoxolan-2-yl]methyl

CAS Registry Number

Not Available

SMILES

[Co+3].[CH2]C1OC(C(O)C1O)N1C=NC2=C(N)N=CN=C12.[H][C@](C)(O)CN=C(O)CC[C@@]1(C)C2=N[C@]([H])([C@]1([H])CC(O)=N)[C@]1(C)NC(=C(C)C3=NC(=CC4=NC(=C2C)[C@@]([H])(CCC(O)=N)C4(C)C)[C@@]([H])(CCC([NH-])=O)[C@]3(C)CC(O)=N)[C@@]([H])(CCC(O)=N)[C@]1(C)CC(O)=N

InChI Identifier

InChI=1S/C48H73N11O8.C10H12N5O3.Co/c1-23(60)22-55-38(67)16-17-45(6)29(18-35(52)64)43-48(9)47(8,21-37(54)66)28(12-15-34(51)63)40(59-48)25(3)42-46(7,20-36(53)65)26(10-13-32(49)61)30(56-42)19-31-44(4,5)27(11-14-33(50)62)39(57-31)24(2)41(45)58-43;1-4-6(16)7(17)10(18-4)15-3-14-5-8(11)12-2-13-9(5)15;/h19,23,26-29,43,60H,10-18,20-22H2,1-9H3,(H14,49,50,51,52,53,54,55,56,57,58,59,61,62,63,64,65,66,67);2-4,6-7,10,16-17H,1H2,(H2,11,12,13);/q;;+3/p-1/t23-,26-,27-,28-,29+,43-,45-,46+,47+,48+;;/m1../s1

InChI Key

PAUPKJHCFVPREX-VUCSARQQSA-M

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as metallotetrapyrroles. These are polycyclic compounds containing a tetrapyrrole skeleton combined with a metal atom.

Kingdom

Organic compounds

Super Class

Organoheterocyclic compounds

Class

Tetrapyrroles and derivatives

Sub Class

Metallotetrapyrroles

Direct Parent

Metallotetrapyrroles

Alternative Parents

Substituents

Metallotetrapyrrole skeleton
5'-deoxyribonucleoside
Glycosyl compound
N-glycosyl compound
6-aminopurine
Pentose monosaccharide
Imidazopyrimidine
Purine
Aminopyrimidine
Fatty amide
Monosaccharide
N-substituted imidazole
Pyrimidine
Imidolactam
Fatty acyl
Azole
Tetrahydrofuran
Pyrroline
Pyrrolidine
Imidazole
Heteroaromatic compound
Carboxamide group
Secondary carboxylic acid amide
Secondary alcohol
Amino acid or derivatives
Primary carboxylic acid amide
Ketimine
Azacycle
Organic metal salt
Organic transition metal salt
Carboxylic acid derivative
Oxacycle
Organooxygen compound
Organonitrogen compound
Alcohol
Hydrocarbon derivative
Primary amine
Imine
Organic oxide
Transition metal alkyl
Organopnictogen compound
Organic nitrogen compound
Organic cobalt salt
Carbonyl group
Organic salt
Organic oxygen compound
Amine
Organic transition metal moeity
Organometallic compound
Organic cation
Aromatic heteropolycyclic compound

Molecular Framework

Aromatic heteropolycyclic compounds

External Descriptors

Not Available

Functional Ontology

Not Available

Physical Properties

State

Solid

Predicted Properties

Property	Value	Source
Water Solubility	0.027 g/L	ALOGPS
logP	2.73	ALOGPS
logP	-2.6	ChemAxon
logS	-4.6	ALOGPS
pKa (Strongest Acidic)	4.97	ChemAxon
pKa (Strongest Basic)	9.07	ChemAxon
Physiological Charge	3	ChemAxon
Hydrogen Acceptor Count	19	ChemAxon
Hydrogen Donor Count	14	ChemAxon
Polar Surface Area	359.63 Å²	ChemAxon
Rotatable Bond Count	21	ChemAxon
Refractivity	308.41 m³·mol⁻¹	ChemAxon
Polarizability	100.62 Å³	ChemAxon
Number of Rings	8	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 GC-MS	Predicted GC-MS Spectrum - GC-MS (TMS_3_2) - 70eV, Positive	Not Available	2022-08-08	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 100 MHz, H₂O, predicted)		2022-08-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 100 MHz, H₂O, predicted)		2022-08-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 1000 MHz, H₂O, predicted)		2022-08-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 1000 MHz, H₂O, predicted)		2022-08-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 200 MHz, H₂O, predicted)		2022-08-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 200 MHz, H₂O, predicted)		2022-08-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 300 MHz, H₂O, predicted)		2022-08-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 300 MHz, H₂O, predicted)		2022-08-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 400 MHz, H₂O, predicted)		2022-08-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 400 MHz, H₂O, predicted)		2022-08-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 500 MHz, H₂O, predicted)		2022-08-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 500 MHz, H₂O, predicted)		2022-08-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 600 MHz, H₂O, predicted)		2022-08-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 600 MHz, H₂O, predicted)		2022-08-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 700 MHz, H₂O, predicted)		2022-08-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 700 MHz, H₂O, predicted)		2022-08-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 800 MHz, H₂O, predicted)		2022-08-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 800 MHz, H₂O, predicted)		2022-08-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 900 MHz, H₂O, predicted)		2022-08-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 900 MHz, H₂O, predicted)		2022-08-20	View Spectrum

Biological Properties

Cellular Locations

Not Available

Biospecimen Locations

Feces

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

Reactions

Reaction ID	Precursor	Product	Enzyme	Data Source	Reference
MMDBr0006898	Adenosyl cobyrinate a,c diamide	Adenosyl cobinamide	Not Available	VMH	30371894
MMDBr0006901	Adenosyl cobinamide	Adenosyl cobinamide phosphate	Not Available	VMH	30371894
MMDBr0006902	Adenosyl cobinamide	Adenosyl cobinamide phosphate	Not Available	VMH	30371894
MMDBr0006909	Cobinamide	Adenosyl cobinamide	Not Available	VMH	30371894
MMDBr0008431	Adenosyl cobyrinate a,c diamide	Adenosyl cobinamide	Not Available	VMH	30371894

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	167	Human feces; Human ; Human sputum; Human unknown; Pig ; Human pleural fluid plaque; Human dental plaque; Human nasal swab; Human feces; pleural fluid plaque; bal; Human stool	Unknown; Metabolic reconstruction
Bacteria	Verrucomicrobia	1	Human ; Human feces	Metabolic reconstruction
Bacteria	Synergistetes	3	Human feces	Metabolic reconstruction
Bacteria	Firmicutes	340	Human feces; Human ; Human stool; Human saliva; Pig ; Human subgingival plaque; Cattle ; Human pleural fluid plaque	Metabolic reconstruction
Bacteria	Bacteroidetes	115	Human feces; Human ; Human appendix biopsy; Human gastric fluid; Human saliva; Human subgingival plaque; Human supragingival plaque; Human stool	Metabolic reconstruction
Bacteria	Spirochaetes	1	Human feces	Metabolic reconstruction
Archaea	Thaumarchaeota	1		Metabolic reconstruction
Bacteria	Fusobacteria	19	Human feces; Human	Metabolic reconstruction
Bacteria	Actinobacteria	105	Human feces; Human ; Human pleural fluid plaque; Human dental plaque; Human sputum; Human nasopharyngeal swab; Human supragingival plaque; Human mucosa; Human subgingival plaque; Human saliva	Metabolic reconstruction
Archaea	Euryarchaeota	5		Metabolic reconstruction
Archaea	Crenarchaeota	1		Metabolic reconstruction
Bacteria	Tenericutes	4	Human feces	Metabolic reconstruction
Bacteria	Planctomycetes	1	Human feces	Metabolic reconstruction
Archaea/Archaea	Euryarchaeota	2		Metabolic reconstruction

Exposure Sources

Host Biospecimen and Location

Host and Biospecimen	Status	Mean	Std	Min	Max	Units	Age	Sex	Health Condition	Data Source	Reference
Human Feces	Detected but not Quantified									HMDB

External Links

HMDB ID

Not Available

DrugBank ID

Not Available

Phenol Explorer Compound ID

Not Available

FooDB ID

FDB024150

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

Not Available

PDB ID

Not Available

ChEBI ID

Not Available

Food Biomarker Ontology

Not Available

References

Synthesis Reference

Not Available

General References

Noronha A, Modamio J, Jarosz Y, Guerard E, Sompairac N, Preciat G, Danielsdottir AD, Krecke M, Merten D, Haraldsdottir HS, Heinken A, Heirendt L, Magnusdottir S, Ravcheev DA, Sahoo S, Gawron P, Friscioni L, Garcia B, Prendergast M, Puente A, Rodrigues M, Roy A, Rouquaya M, Wiltgen L, Zagare A, John E, Krueger M, Kuperstein I, Zinovyev A, Schneider R, Fleming RMT, Thiele I: The Virtual Metabolic Human database: integrating human and gut microbiome metabolism with nutrition and disease. Nucleic Acids Res. 2019 Jan 8;47(D1):D614-D624. doi: 10.1093/nar/gky992. [PubMed:30371894 ]
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 Adenosyl cobinamide (MMDBc0029849)

MOL for #<Metabolite:0x00007fdb10a9bb70>

3D MOL for #<Metabolite:0x00007fdb10a9bb70>

3D SDF for #<Metabolite:0x00007fdb10a9bb70>

3D-SDF for #<Metabolite:0x00007fdb10a9bb70>

PDB for #<Metabolite:0x00007fdb10a9bb70>

3D PDB for #<Metabolite:0x00007fdb10a9bb70>

SMILES for #<Metabolite:0x00007fdb10a9bb70>

INCHI for #<Metabolite:0x00007fdb10a9bb70>

Structure for #<Metabolite:0x00007fdb10a9bb70>

3D Structure for #<Metabolite:0x00007fdb10a9bb70>