MiMeDB: Showing metabocard for GDP-4-dehydro-6-deoxy-Œ±-D-mannose (MMDBc0032162)

Record Information

Version

1.0

Status

Detected and Quantified

Creation Date

2021-11-18 02:04:58 UTC

Update Date

2022-08-31 18:31:01 UTC

Metabolite ID

MMDBc0032162

Metabolite Identification

Common Name

GDP-4-dehydro-6-deoxy-Œ±-D-mannose

Description

GDP-4-dehydro-6-deoxy-alpha-D-mannose is an intermediate in GDP-L-fucose biosynthesis I (from GDP-D-mannose) in E.coli. It is a substrate for the enzyme GDP-fucose synthase which catalyzes the reaction GDP-4-dehydro-6-deoxy-alpha-D-mannose + NADPH + H+ -> GDP-beta-L-fucose + NADP+. It is also a product for enzyme GDP-mannose 4,6-dehydratase which catalyzes reaction GDP-alpha-D-mannose -> GDP-4-dehydro-6-deoxy-alpha-D-mannose + H2O (BioCYc compound: GDP-4-DEHYDRO-6-DEOXY-D-MANNOSE).

Structure

MOL SDF PDB SMILES InChI

      
  Mrv1533005261516302D          

 46 49  0  0  0  0            999 V2000
   -4.2767   -3.0424    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3583    0.6875    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.8637    3.7045    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.5230   -3.3779    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    0.3091    1.1725    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    2.1333    4.1170    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.4368   -4.1984    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.0937    0.9175    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
   -2.6831   -4.5340    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    1.5786    1.5850    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
   -2.0156   -4.0491    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    2.1333    3.2920    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.8477    4.5295    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.0937    2.2524    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
   -2.1019   -3.2286    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    3.5622    3.2920    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.2767    2.8795    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    1.3486    4.3719    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    2.8477    2.8795    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    3.5622    4.1170    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    1.3486    3.0370    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   -4.1042   -4.6833    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.3486    0.1329    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.5968   -5.3545    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.4036    1.5850    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2620   -4.3846    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.8477    5.3545    0.0000 O   0  5  0  0  0  0  0  0  0  0  0  0
   -1.4244    0.0496    0.0000 O   0  5  0  0  0  0  0  0  0  0  0  0
   -0.4545   -1.2852    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3412   -2.0094    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7002   -1.8369    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2720   -0.1328    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8556   -2.8930    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.3091    1.9975    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4344   -2.7437    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6069   -1.1027    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9395   -0.6178    0.0000 P   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5207   -1.9232    0.0000 P   0  0  0  0  0  0  0  0  0  0  0  0
   -4.1904   -3.8629    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.4381    0.3576    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.9085    0.7885    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.3505   -5.0189    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.9532    2.3200    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9294   -4.8695    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.5103    2.8358    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3482   -3.5641    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
  4  1  1  1  0  0  0
  5  2  1  1  0  0  0
  7  4  1  0  0  0  0
  8  5  1  0  0  0  0
  9  7  1  0  0  0  0
 10  8  1  0  0  0  0
 11  9  1  0  0  0  0
 12  6  2  0  0  0  0
 13  6  1  0  0  0  0
 14 10  1  0  0  0  0
 15 11  1  0  0  0  0
 17 16  2  0  0  0  0
 18  3  2  0  0  0  0
 18  6  1  0  0  0  0
 19 12  1  0  0  0  0
 19 16  1  0  0  0  0
 20 13  2  0  0  0  0
 20 16  1  0  0  0  0
 21  3  1  0  0  0  0
 21 12  1  0  0  0  0
 14 21  1  1  0  0  0
 22  7  2  0  0  0  0
  8 23  1  6  0  0  0
  9 24  1  1  0  0  0
 10 25  1  6  0  0  0
 11 26  1  1  0  0  0
 27 13  1  0  0  0  0
 32  2  1  0  0  0  0
 33  4  1  0  0  0  0
 33 15  1  0  0  0  0
 34  5  1  0  0  0  0
 34 14  1  0  0  0  0
 15 35  1  6  0  0  0
 37 28  1  0  0  0  0
 37 29  2  0  0  0  0
 37 32  1  0  0  0  0
 37 36  1  0  0  0  0
 38 30  1  0  0  0  0
 38 31  2  0  0  0  0
 38 35  1  0  0  0  0
 38 36  1  0  0  0  0
  4 39  1  6  0  0  0
  5 40  1  6  0  0  0
  8 41  1  1  0  0  0
  9 42  1  6  0  0  0
 10 43  1  1  0  0  0
 11 44  1  6  0  0  0
 14 45  1  6  0  0  0
 15 46  1  1  0  0  0
M  CHG  2  27  -1  28  -1
M  END

      
  Mrv1533005261516302D          

 46 49  0  0  0  0            999 V2000
   -4.2767   -3.0424    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3583    0.6875    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.8637    3.7045    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.5230   -3.3779    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    0.3091    1.1725    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    2.1333    4.1170    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.4368   -4.1984    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.0937    0.9175    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
   -2.6831   -4.5340    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    1.5786    1.5850    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
   -2.0156   -4.0491    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    2.1333    3.2920    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.8477    4.5295    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.0937    2.2524    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
   -2.1019   -3.2286    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    3.5622    3.2920    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.2767    2.8795    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    1.3486    4.3719    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    2.8477    2.8795    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    3.5622    4.1170    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    1.3486    3.0370    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   -4.1042   -4.6833    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.3486    0.1329    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.5968   -5.3545    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.4036    1.5850    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2620   -4.3846    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.8477    5.3545    0.0000 O   0  5  0  0  0  0  0  0  0  0  0  0
   -1.4244    0.0496    0.0000 O   0  5  0  0  0  0  0  0  0  0  0  0
   -0.4545   -1.2852    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3412   -2.0094    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7002   -1.8369    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2720   -0.1328    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8556   -2.8930    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.3091    1.9975    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4344   -2.7437    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6069   -1.1027    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9395   -0.6178    0.0000 P   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5207   -1.9232    0.0000 P   0  0  0  0  0  0  0  0  0  0  0  0
   -4.1904   -3.8629    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.4381    0.3576    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.9085    0.7885    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.3505   -5.0189    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.9532    2.3200    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9294   -4.8695    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.5103    2.8358    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3482   -3.5641    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
  4  1  1  1  0  0  0
  5  2  1  1  0  0  0
  7  4  1  0  0  0  0
  8  5  1  0  0  0  0
  9  7  1  0  0  0  0
 10  8  1  0  0  0  0
 11  9  1  0  0  0  0
 12  6  2  0  0  0  0
 13  6  1  0  0  0  0
 14 10  1  0  0  0  0
 15 11  1  0  0  0  0
 17 16  2  0  0  0  0
 18  3  2  0  0  0  0
 18  6  1  0  0  0  0
 19 12  1  0  0  0  0
 19 16  1  0  0  0  0
 20 13  2  0  0  0  0
 20 16  1  0  0  0  0
 21  3  1  0  0  0  0
 21 12  1  0  0  0  0
 14 21  1  1  0  0  0
 22  7  2  0  0  0  0
  8 23  1  6  0  0  0
  9 24  1  1  0  0  0
 10 25  1  6  0  0  0
 11 26  1  1  0  0  0
 27 13  1  0  0  0  0
 32  2  1  0  0  0  0
 33  4  1  0  0  0  0
 33 15  1  0  0  0  0
 34  5  1  0  0  0  0
 34 14  1  0  0  0  0
 15 35  1  6  0  0  0
 37 28  1  0  0  0  0
 37 29  2  0  0  0  0
 37 32  1  0  0  0  0
 37 36  1  0  0  0  0
 38 30  1  0  0  0  0
 38 31  2  0  0  0  0
 38 35  1  0  0  0  0
 38 36  1  0  0  0  0
  4 39  1  6  0  0  0
  5 40  1  6  0  0  0
  8 41  1  1  0  0  0
  9 42  1  6  0  0  0
 10 43  1  1  0  0  0
 11 44  1  6  0  0  0
 14 45  1  6  0  0  0
 15 46  1  1  0  0  0
M  CHG  2  27  -1  28  -1
M  END
> <DATABASE_ID>
MMDBc0032162

> <DATABASE_NAME>
MIME

> <SMILES>
[H][C@]1(COP([O-])(=O)OP(O)(=O)O[C@@]2([H])O[C@]([H])(C)C(=O)[C@]([H])(O)[C@]2([H])O)O[C@@]([H])(N2C=NC3=C2NC(=N)N=C3[O-])[C@]([H])(O)[C@]1([H])O

> <INCHI_IDENTIFIER>
InChI=1S/C16H23N5O15P2/c1-4-7(22)9(24)11(26)15(33-4)35-38(30,31)36-37(28,29)32-2-5-8(23)10(25)14(34-5)21-3-18-6-12(21)19-16(17)20-13(6)27/h3-5,8-11,14-15,23-26H,2H2,1H3,(H,28,29)(H,30,31)(H3,17,19,20,27)/p-2/t4-,5-,8-,9+,10-,11+,14-,15-/m1/s1

> <INCHI_KEY>
PNHLMHWWFOPQLK-BKUUWRAGSA-L

> <FORMULA>
C16H21N5O15P2

> <MOLECULAR_WEIGHT>
585.313

> <EXACT_MASS>
585.052036152

> <JCHEM_ACCEPTOR_COUNT>
16

> <JCHEM_ATOM_COUNT>
59

> <JCHEM_AVERAGE_POLARIZABILITY>
48.473797317953746

> <JCHEM_BIOAVAILABILITY>
0

> <JCHEM_DONOR_COUNT>
7

> <JCHEM_FORMAL_CHARGE>
-2

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
9-[(2R,3R,4S,5R)-5-{[({[(2R,3S,4R,6R)-3,4-dihydroxy-6-methyl-5-oxooxan-2-yl]oxy}(hydroxy)phosphoryl phosphonato)oxy]methyl}-3,4-dihydroxyoxolan-2-yl]-2-imino-3,9-dihydro-2H-purin-6-olate

> <ALOGPS_LOGP>
-1.36

> <JCHEM_LOGP>
-4.131213652552748

> <ALOGPS_LOGS>
-1.91

> <JCHEM_MDDR_LIKE_RULE>
1

> <JCHEM_NUMBER_OF_RINGS>
4

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-2

> <JCHEM_PKA>
3.38388287712154

> <JCHEM_PKA_STRONGEST_ACIDIC>
1.7077879720906535

> <JCHEM_PKA_STRONGEST_BASIC>
2.7816200495657326

> <JCHEM_POLAR_SURFACE_AREA>
310.69000000000005

> <JCHEM_REFRACTIVITY>
136.21059999999997

> <JCHEM_ROTATABLE_BOND_COUNT>
8

> <JCHEM_RULE_OF_FIVE>
0

> <ALOGPS_SOLUBILITY>
7.65e+00 g/l

> <JCHEM_TRADITIONAL_IUPAC>
9-[(2R,3R,4S,5R)-5-[({[(2R,3S,4R,6R)-3,4-dihydroxy-6-methyl-5-oxooxan-2-yl]oxy(hydroxy)phosphoryl phosphonato}oxy)methyl]-3,4-dihydroxyoxolan-2-yl]-2-imino-3H-purin-6-olate

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 26-MAY-15   NONE
TITLE     NULL                                                        
COMPND    MOLECULE:                                                   
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   26-MAY-15         0                                  
HETATM    1  C   UNK     0      -7.983  -5.679   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0      -0.669   1.283   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       1.612   6.915   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0      -6.576  -6.305   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       0.577   2.189   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       3.982   7.685   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0      -6.415  -7.837   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0       2.042   1.713   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0      -5.008  -8.463   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0       2.947   2.959   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0      -3.762  -7.558   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0       3.982   6.145   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0       5.316   8.455   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0       2.042   4.204   0.000  0.00  0.00           C+0
HETATM   15  C   UNK     0      -3.924  -6.027   0.000  0.00  0.00           C+0
HETATM   16  C   UNK     0       6.649   6.145   0.000  0.00  0.00           C+0
HETATM   17  N   UNK     0       7.983   5.375   0.000  0.00  0.00           N+0
HETATM   18  N   UNK     0       2.517   8.161   0.000  0.00  0.00           N+0
HETATM   19  N   UNK     0       5.316   5.375   0.000  0.00  0.00           N+0
HETATM   20  N   UNK     0       6.649   7.685   0.000  0.00  0.00           N+0
HETATM   21  N   UNK     0       2.517   5.669   0.000  0.00  0.00           N+0
HETATM   22  O   UNK     0      -7.661  -8.742   0.000  0.00  0.00           O+0
HETATM   23  O   UNK     0       2.517   0.248   0.000  0.00  0.00           O+0
HETATM   24  O   UNK     0      -4.847  -9.995   0.000  0.00  0.00           O+0
HETATM   25  O   UNK     0       4.487   2.959   0.000  0.00  0.00           O+0
HETATM   26  O   UNK     0      -2.356  -8.185   0.000  0.00  0.00           O+0
HETATM   27  O   UNK     0       5.316   9.995   0.000  0.00  0.00           O-1
HETATM   28  O   UNK     0      -2.659   0.093   0.000  0.00  0.00           O-1
HETATM   29  O   UNK     0      -0.848  -2.399   0.000  0.00  0.00           O+0
HETATM   30  O   UNK     0      -4.370  -3.751   0.000  0.00  0.00           O+0
HETATM   31  O   UNK     0      -1.307  -3.429   0.000  0.00  0.00           O+0
HETATM   32  O   UNK     0      -0.508  -0.248   0.000  0.00  0.00           O+0
HETATM   33  O   UNK     0      -5.330  -5.400   0.000  0.00  0.00           O+0
HETATM   34  O   UNK     0       0.577   3.729   0.000  0.00  0.00           O+0
HETATM   35  O   UNK     0      -2.678  -5.122   0.000  0.00  0.00           O+0
HETATM   36  O   UNK     0      -3.000  -2.058   0.000  0.00  0.00           O+0
HETATM   37  P   UNK     0      -1.754  -1.153   0.000  0.00  0.00           P+0
HETATM   38  P   UNK     0      -2.839  -3.590   0.000  0.00  0.00           P+0
HETATM   39  H   UNK     0      -7.822  -7.211   0.000  0.00  0.00           H+0
HETATM   40  H   UNK     0       0.818   0.668   0.000  0.00  0.00           H+0
HETATM   41  H   UNK     0       3.563   1.472   0.000  0.00  0.00           H+0
HETATM   42  H   UNK     0      -6.254  -9.369   0.000  0.00  0.00           H+0
HETATM   43  H   UNK     0       3.646   4.331   0.000  0.00  0.00           H+0
HETATM   44  H   UNK     0      -3.602  -9.090   0.000  0.00  0.00           H+0
HETATM   45  H   UNK     0       0.953   5.293   0.000  0.00  0.00           H+0
HETATM   46  H   UNK     0      -2.517  -6.653   0.000  0.00  0.00           H+0
CONECT    1    4                                                            
CONECT    2    5   32                                                       
CONECT    3   18   21                                                       
CONECT    4    1    7   33   39                                             
CONECT    5    2    8   34   40                                             
CONECT    6   12   13   18                                                  
CONECT    7    4    9   22                                                  
CONECT    8    5   10   23   41                                             
CONECT    9    7   11   24   42                                             
CONECT   10    8   14   25   43                                             
CONECT   11    9   15   26   44                                             
CONECT   12    6   19   21                                                  
CONECT   13    6   20   27                                                  
CONECT   14   10   21   34   45                                             
CONECT   15   11   33   35   46                                             
CONECT   16   17   19   20                                                  
CONECT   17   16                                                            
CONECT   18    3    6                                                       
CONECT   19   12   16                                                       
CONECT   20   13   16                                                       
CONECT   21    3   12   14                                                  
CONECT   22    7                                                            
CONECT   23    8                                                            
CONECT   24    9                                                            
CONECT   25   10                                                            
CONECT   26   11                                                            
CONECT   27   13                                                            
CONECT   28   37                                                            
CONECT   29   37                                                            
CONECT   30   38                                                            
CONECT   31   38                                                            
CONECT   32    2   37                                                       
CONECT   33    4   15                                                       
CONECT   34    5   14                                                       
CONECT   35   15   38                                                       
CONECT   36   37   38                                                       
CONECT   37   28   29   32   36                                             
CONECT   38   30   31   35   36                                             
CONECT   39    4                                                            
CONECT   40    5                                                            
CONECT   41    8                                                            
CONECT   42    9                                                            
CONECT   43   10                                                            
CONECT   44   11                                                            
CONECT   45   14                                                            
CONECT   46   15                                                            
MASTER        0    0    0    0    0    0    0    0   46    0   98    0
END

Synonyms

Value	Source
GDP-4-Dehydro-6-deoxy-alpha-D-mannose dianion	ChEBI
GDP-4-Dehydro-alpha-D-rhamnose	ChEBI
GDP-4-Dehydro-6-deoxy-a-D-mannose dianion	Generator
GDP-4-Dehydro-6-deoxy-α-D-mannose dianion	Generator
GDP-4-Dehydro-a-D-rhamnose	Generator
GDP-4-Dehydro-α-D-rhamnose	Generator
GDP-4-dehydro-6-Deoxy-a-D-mannose(2-)	Generator
GDP-4-dehydro-6-Deoxy-α-D-mannose(2-)	Generator

Molecular Formula

C₁₆H₂₁N₅O₁₅P₂

Average Mass

585.313

Monoisotopic Mass

585.052036152

IUPAC Name

9-[(2R,3R,4S,5R)-5-{[({[(2R,3S,4R,6R)-3,4-dihydroxy-6-methyl-5-oxooxan-2-yl]oxy}(hydroxy)phosphoryl phosphonato)oxy]methyl}-3,4-dihydroxyoxolan-2-yl]-2-imino-3,9-dihydro-2H-purin-6-olate

Traditional Name

9-[(2R,3R,4S,5R)-5-[({[(2R,3S,4R,6R)-3,4-dihydroxy-6-methyl-5-oxooxan-2-yl]oxy(hydroxy)phosphoryl phosphonato}oxy)methyl]-3,4-dihydroxyoxolan-2-yl]-2-imino-3H-purin-6-olate

CAS Registry Number

Not Available

SMILES

[H][C@]1(COP([O-])(=O)OP(O)(=O)O[C@@]2([H])O[C@]([H])(C)C(=O)[C@]([H])(O)[C@]2([H])O)O[C@@]([H])(N2C=NC3=C2NC(=N)N=C3[O-])[C@]([H])(O)[C@]1([H])O

InChI Identifier

InChI=1S/C16H23N5O15P2/c1-4-7(22)9(24)11(26)15(33-4)35-38(30,31)36-37(28,29)32-2-5-8(23)10(25)14(34-5)21-3-18-6-12(21)19-16(17)20-13(6)27/h3-5,8-11,14-15,23-26H,2H2,1H3,(H,28,29)(H,30,31)(H3,17,19,20,27)/p-2/t4-,5-,8-,9+,10-,11+,14-,15-/m1/s1

InChI Key

PNHLMHWWFOPQLK-BKUUWRAGSA-L

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as purine nucleotide sugars. These are purine nucleotides bound to a saccharide derivative through the terminal phosphate group.

Kingdom

Organic compounds

Super Class

Nucleosides, nucleotides, and analogues

Class

Purine nucleotides

Sub Class

Purine nucleotide sugars

Direct Parent

Purine nucleotide sugars

Alternative Parents

Substituents

Purine nucleotide sugar
Purine ribonucleoside diphosphate
Purine ribonucleoside monophosphate
Pentose phosphate
Pentose-5-phosphate
Glycosyl compound
N-glycosyl compound
6-oxopurine
Hypoxanthine
Monosaccharide phosphate
Organic pyrophosphate
Imidazopyrimidine
Purine
Aminopyrimidine
Pyrimidone
Monosaccharide
N-substituted imidazole
Organic phosphoric acid derivative
Oxane
Phosphoric acid ester
Alkyl phosphate
Pyrimidine
Vinylogous amide
Tetrahydrofuran
Azole
Imidazole
Heteroaromatic compound
Secondary alcohol
Cyclic ketone
Ketone
Organoheterocyclic compound
Azacycle
Oxacycle
Carbonyl group
Organic oxygen compound
Organic nitrogen compound
Alcohol
Amine
Hydrocarbon derivative
Organic oxide
Organopnictogen compound
Primary amine
Organonitrogen compound
Organooxygen compound
Organic anion
Aromatic heteropolycyclic compound

Molecular Framework

Aromatic heteropolycyclic compounds

External Descriptors

nucleotide-sugar oxoanion (CHEBI:57964 )

Functional Ontology

Not Available

Physical Properties

State

Expected Solid

Predicted Properties

Property	Value	Source
Water Solubility	7.65 g/L	ALOGPS
logP	-1.4	ALOGPS
logP	-4.1	ChemAxon
logS	-1.9	ALOGPS
pKa (Strongest Acidic)	1.71	ChemAxon
pKa (Strongest Basic)	2.78	ChemAxon
Physiological Charge	-2	ChemAxon
Hydrogen Acceptor Count	16	ChemAxon
Hydrogen Donor Count	7	ChemAxon
Polar Surface Area	310.69 Å²	ChemAxon
Rotatable Bond Count	8	ChemAxon
Refractivity	136.21 m³·mol⁻¹	ChemAxon
Polarizability	48.47 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	splash10-000i-0200090000-388df5902bd673b3f3ec	2015-09-15	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Positive	splash10-00lr-0021090000-09b9315c6b1960463a08	2015-09-15	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Positive	splash10-0007-9200000000-f600218625e165154ea7	2015-09-15	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Negative	splash10-001i-3200090000-60e2b5e121b22d2dc63c	2015-09-15	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Negative	splash10-001i-9600070000-3c1170b42c3cc3f43e7e	2015-09-15	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Negative	splash10-0a4i-9100000000-3ec23c48e32bfc246243	2015-09-15	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

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
MMDBr0012931	GDP-6-deoxy-alpha-D-talose	GDP-4-dehydro-6-deoxy-Œ±-D-mannose	GDP-6-deoxy-D-talose 4-dehydrogenase	Dehydrogenation	RHEA	34755880
MMDBr0012932	GDP-6-deoxy-alpha-D-talose	GDP-4-dehydro-6-deoxy-Œ±-D-mannose	GDP-6-deoxy-D-talose 4-dehydrogenase	Dehydrogenation	RHEA	34755880
MMDBr0013255	GDP-alpha-D-rhamnose	GDP-4-dehydro-6-deoxy-Œ±-D-mannose	GDP-6-deoxy-D-mannose reductase	Reduction	RHEA	34755880
MMDBr0013256	GDP-alpha-D-rhamnose	GDP-4-dehydro-6-deoxy-Œ±-D-mannose	GDP-6-deoxy-D-mannose reductase	Reduction	RHEA	34755880
MMDBr0013818	GDP-beta-L-fucose	GDP-4-dehydro-6-deoxy-Œ±-D-mannose	GDP-L-fucose synthase	Synthesis	RHEA	34755880
MMDBr0014384	Guanosine diphosphate mannose	GDP-4-dehydro-6-deoxy-Œ±-D-mannose	GDP-mannose 4,6-dehydratase	Hydration/dehydration of C-O bond	RHEA	34755880
MMDBr0015538	alpha-Ketoglutarate	GDP-4-dehydro-6-deoxy-Œ±-D-mannose	GDP-perosamine synthase	Synthesis	RHEA	34755880
MMDBr0016454	GDP-4-dehydro-6-deoxy-Œ±-D-mannose	alpha-Ketoglutarate	GDP-4-keto-6-deoxy-D-mannose 3-dehydratase	Hydration/dehydration of C-O bond	RHEA	34755880
MMDBr0018480	Guanosine diphosphate mannose	Water	GDP-mannose 4,6-dehydratase	Hydration/dehydration of C-O bond	PathBank	31602464
MMDBr0018481	Hydrogen Ion	NADP	GDP-L-fucose synthase	Synthesis	PathBank	31602464

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	15	Human ; Human feces; Human feces; pleural fluid plaque; bal; Human stool; Human subgingival plaque; Human saliva	Unknown
Bacteria/NULL	Firmicutes	1
Eukaryota/Fungi	Ascomycota	1

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

25243979

PDB ID

Not Available

ChEBI ID

57964

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 GDP-4-dehydro-6-deoxy-Œ±-D-mannose (MMDBc0032162)

MOL for #<Metabolite:0x000055c79c68a0b0>

3D MOL for #<Metabolite:0x000055c79c68a0b0>

3D SDF for #<Metabolite:0x000055c79c68a0b0>

3D-SDF for #<Metabolite:0x000055c79c68a0b0>

PDB for #<Metabolite:0x000055c79c68a0b0>

3D PDB for #<Metabolite:0x000055c79c68a0b0>

SMILES for #<Metabolite:0x000055c79c68a0b0>

INCHI for #<Metabolite:0x000055c79c68a0b0>

Structure for #<Metabolite:0x000055c79c68a0b0>

3D Structure for #<Metabolite:0x000055c79c68a0b0>