MiMeDB: Showing metabocard for 8-oxo-dGDP (MMDBc0054308)

Record Information

Version

1.0

Status

Detected and Quantified

Creation Date

2022-06-05 23:06:17 UTC

Update Date

2022-09-01 02:28:24 UTC

Metabolite ID

MMDBc0054308

Metabolite Identification

Common Name

8-oxo-dGDP

Description

8-oxo-dGDP belongs to the class of organic compounds known as purine 2'-deoxyribonucleoside diphosphates. These are purine nucleotides with diphosphate group linked to the ribose moiety lacking a hydroxyl group at position 2. 8-oxo-dGDP is a very strong basic compound (based on its pKa). In humans, 8-oxo-dGDP is involved in the metabolic disorder called the purine nucleoside phosphorylase deficiency pathway. 8-oxo-dgdp is part of the Purine metabolism pathway.

Structure

MOL 3D MOL SDF 3D SDF PDB 3D PDB SMILES InChI


  Mrv0541 10301209532D          

 31 33  0  0  0  0            999 V2000
   -1.1831   -2.4049    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1435   -4.2695    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1831   -3.2299    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
   -0.3984   -3.4849    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
   -0.3984   -2.1500    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    0.6411   -0.2854    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.6411   -1.1104    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.3556    0.1271    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.0701   -1.1104    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6284   -0.6979    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.7845   -1.5229    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1435   -0.0305    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    1.3556   -1.5229    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    2.0701   -0.2854    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1435   -1.3654    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8505   -3.7149    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.3556    0.9521    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4534   -0.6979    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.7873   -6.3533    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.8088   -6.9888    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.1518   -5.3748    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.1338   -5.4806    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.7030   -4.9707    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.6635   -4.4410    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.0865   -2.8174    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.1733   -6.0103    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.9803   -6.1818    0.0000 P   0  0  0  0  0  0  0  0  0  0  0  0
    0.9184   -5.2257    0.0000 P   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9181   -2.8554    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9818   -4.0682    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9818   -1.5666    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
  3  1  1  0  0  0  0
  4  2  1  6  0  0  0
  4  3  1  0  0  0  0
  5  1  1  0  0  0  0
  7  6  2  0  0  0  0
  8  6  1  0  0  0  0
 11  9  2  0  0  0  0
 12  6  1  0  0  0  0
 12 10  2  0  0  0  0
 13  7  1  0  0  0  0
 13  9  1  0  0  0  0
 14  8  2  0  0  0  0
 14  9  1  0  0  0  0
  5 15  1  6  0  0  0
 15  7  1  0  0  0  0
 15 10  1  0  0  0  0
  3 16  1  1  0  0  0
 17  8  1  0  0  0  0
 18 10  1  0  0  0  0
 24  2  1  0  0  0  0
 25  4  1  0  0  0  0
 25  5  1  0  0  0  0
 27 19  1  0  0  0  0
 27 20  1  0  0  0  0
 27 21  2  0  0  0  0
 27 26  1  0  0  0  0
 28 22  1  0  0  0  0
 28 23  2  0  0  0  0
 28 24  1  0  0  0  0
 28 26  1  0  0  0  0
  3 29  1  6  0  0  0
  4 30  1  1  0  0  0
  5 31  1  1  0  0  0
M  END

HMDB0059648
     RDKit          3D
8-oxo-dGDP
 43 45  0  0  0  0  0  0  0  0999 V2000
   -6.2188    0.5436   -2.8321 N   0  0  0  0  0  0  0  0  0  0  0  0
   -5.7263    0.2286   -1.6573 C   0  0  0  0  0  0  0  0  0  0  0  0
   -6.5110   -0.2224   -0.6607 N   0  0  0  0  0  0  0  0  0  0  0  0
   -6.0816   -0.5602    0.5538 C   0  0  0  0  0  0  0  0  0  0  0  0
   -6.9248   -1.0241    1.5624 O   0  0  0  0  0  0  0  0  0  0  0  0
   -4.7338   -0.4443    0.8244 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.9944   -0.6933    1.9142 N   0  0  0  0  0  0  0  0  0  0  0  0
   -2.7166   -0.3983    1.6135 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5887   -0.4931    2.4177 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.6698    0.0315    0.3414 N   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4905    0.4539   -0.3877 C   0  0  1  0  0  0  0  0  0  0  0  0
   -0.7613    1.5725    0.3164 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.6162    1.4691   -0.3516 C   0  0  2  0  0  0  0  0  0  0  0  0
    0.6802    2.2665   -1.4887 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.6819    0.0221   -0.6929 C   0  0  1  0  0  0  0  0  0  0  0  0
    1.7770   -0.6830    0.1020 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.9861   -0.0342   -0.1430 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.2653   -0.7243    0.6804 P   0  0  0  0  0  5  0  0  0  0  0  0
    3.8052   -1.5767    1.8518 O   0  0  0  0  0  0  0  0  0  0  0  0
    5.2069    0.5303    1.3276 O   0  0  0  0  0  0  0  0  0  0  0  0
    5.2497   -1.6725   -0.3169 O   0  0  0  0  0  0  0  0  0  0  0  0
    6.5889   -0.8047   -0.8719 P   0  0  0  0  0  5  0  0  0  0  0  0
    6.1997    0.0495   -2.0721 O   0  0  0  0  0  0  0  0  0  0  0  0
    7.8011   -1.8653   -1.3942 O   0  0  0  0  0  0  0  0  0  0  0  0
    7.2083    0.1439    0.3794 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5466   -0.5467   -0.5151 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.9189    0.0204   -0.1996 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.4109    0.3461   -1.4064 N   0  0  0  0  0  0  0  0  0  0  0  0
   -7.2482    0.4260   -2.9516 H   0  0  0  0  0  0  0  0  0  0  0  0
   -6.7285   -1.9392    1.9516 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5257    0.0827    3.2684 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7432    0.8229   -1.3994 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5795    1.3454    1.3865 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2180    2.5613    0.1467 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.4040    1.7762    0.3760 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.4372    1.9052   -2.0381 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.9589   -0.0648   -1.7795 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.5435   -0.5467    1.1792 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.8087   -1.7603   -0.1487 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.1585    1.2908    0.6684 H   0  0  0  0  0  0  0  0  0  0  0  0
    7.5147   -2.7978   -1.2131 H   0  0  0  0  0  0  0  0  0  0  0  0
    8.1746    0.2770    0.3043 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.7297    0.6863   -2.1173 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  2  3
  2  3  1  0
  3  4  2  0
  4  5  1  0
  4  6  1  0
  6  7  1  0
  7  8  2  0
  8  9  1  0
  8 10  1  0
 10 11  1  0
 11 12  1  0
 12 13  1  0
 13 14  1  0
 13 15  1  0
 15 16  1  0
 16 17  1  0
 17 18  1  0
 18 19  2  0
 18 20  1  0
 18 21  1  0
 21 22  1  0
 22 23  2  0
 22 24  1  0
 22 25  1  0
 15 26  1  0
 10 27  1  0
 27 28  1  0
 28  2  1  0
 27  6  2  0
 26 11  1  0
  1 29  1  0
  5 30  1  0
  9 31  1  0
 11 32  1  6
 12 33  1  0
 12 34  1  0
 13 35  1  1
 14 36  1  0
 15 37  1  6
 16 38  1  0
 16 39  1  0
 20 40  1  0
 24 41  1  0
 25 42  1  0
 28 43  1  0
M  END


  Mrv0541 10301209532D          

 31 33  0  0  0  0            999 V2000
   -1.1831   -2.4049    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1435   -4.2695    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1831   -3.2299    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
   -0.3984   -3.4849    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
   -0.3984   -2.1500    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    0.6411   -0.2854    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.6411   -1.1104    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.3556    0.1271    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.0701   -1.1104    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6284   -0.6979    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.7845   -1.5229    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1435   -0.0305    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    1.3556   -1.5229    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    2.0701   -0.2854    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1435   -1.3654    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8505   -3.7149    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.3556    0.9521    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4534   -0.6979    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.7873   -6.3533    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.8088   -6.9888    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.1518   -5.3748    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.1338   -5.4806    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.7030   -4.9707    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.6635   -4.4410    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.0865   -2.8174    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.1733   -6.0103    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.9803   -6.1818    0.0000 P   0  0  0  0  0  0  0  0  0  0  0  0
    0.9184   -5.2257    0.0000 P   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9181   -2.8554    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9818   -4.0682    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9818   -1.5666    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
  3  1  1  0  0  0  0
  4  2  1  6  0  0  0
  4  3  1  0  0  0  0
  5  1  1  0  0  0  0
  7  6  2  0  0  0  0
  8  6  1  0  0  0  0
 11  9  2  0  0  0  0
 12  6  1  0  0  0  0
 12 10  2  0  0  0  0
 13  7  1  0  0  0  0
 13  9  1  0  0  0  0
 14  8  2  0  0  0  0
 14  9  1  0  0  0  0
  5 15  1  6  0  0  0
 15  7  1  0  0  0  0
 15 10  1  0  0  0  0
  3 16  1  1  0  0  0
 17  8  1  0  0  0  0
 18 10  1  0  0  0  0
 24  2  1  0  0  0  0
 25  4  1  0  0  0  0
 25  5  1  0  0  0  0
 27 19  1  0  0  0  0
 27 20  1  0  0  0  0
 27 21  2  0  0  0  0
 27 26  1  0  0  0  0
 28 22  1  0  0  0  0
 28 23  2  0  0  0  0
 28 24  1  0  0  0  0
 28 26  1  0  0  0  0
  3 29  1  6  0  0  0
  4 30  1  1  0  0  0
  5 31  1  1  0  0  0
M  END
> <DATABASE_ID>
MMDBc0054308

> <DATABASE_NAME>
MIME

> <SMILES>
[H][C@]1(O)C[C@@]([H])(O[C@]1([H])COP(O)(=O)OP(O)(O)=O)N1C(O)=NC2=C1NC(=N)N=C2O

> <INCHI_IDENTIFIER>
InChI=1S/C10H15N5O11P2/c11-9-13-7-6(8(17)14-9)12-10(18)15(7)5-1-3(16)4(25-5)2-24-28(22,23)26-27(19,20)21/h3-5,16H,1-2H2,(H,12,18)(H,22,23)(H2,19,20,21)(H3,11,13,14,17)/t3-,4+,5+/m0/s1

> <INCHI_KEY>
LJMLTZSNWOCYNQ-VPENINKCSA-N

> <FORMULA>
C10H15N5O11P2

> <MOLECULAR_WEIGHT>
443.2005

> <EXACT_MASS>
443.024329371

> <JCHEM_ACCEPTOR_COUNT>
13

> <JCHEM_AVERAGE_POLARIZABILITY>
34.87022991256715

> <JCHEM_BIOAVAILABILITY>
0

> <JCHEM_DONOR_COUNT>
8

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
[({[(2R,3S,5R)-5-(6,8-dihydroxy-2-imino-3,9-dihydro-2H-purin-9-yl)-3-hydroxyoxolan-2-yl]methoxy}(hydroxy)phosphoryl)oxy]phosphonic acid

> <ALOGPS_LOGP>
-1.45

> <JCHEM_LOGP>
-1.8732008885516371

> <ALOGPS_LOGS>
-1.90

> <JCHEM_MDDR_LIKE_RULE>
1

> <JCHEM_NUMBER_OF_RINGS>
3

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-3

> <JCHEM_PKA>
3.110682200715929

> <JCHEM_PKA_STRONGEST_ACIDIC>
1.7716579176866856

> <JCHEM_PKA_STRONGEST_BASIC>
5.363617962357166

> <JCHEM_POLAR_SURFACE_AREA>
249.26999999999995

> <JCHEM_REFRACTIVITY>
96.89149999999998

> <JCHEM_ROTATABLE_BOND_COUNT>
6

> <JCHEM_RULE_OF_FIVE>
0

> <ALOGPS_SOLUBILITY>
5.62e+00 g/l

> <JCHEM_TRADITIONAL_IUPAC>
{[(2R,3S,5R)-5-(6,8-dihydroxy-2-imino-3H-purin-9-yl)-3-hydroxyoxolan-2-yl]methoxy(hydroxy)phosphoryl}oxyphosphonic acid

> <JCHEM_VEBER_RULE>
0

$$$$

HMDB0059648
     RDKit          3D
8-oxo-dGDP
 43 45  0  0  0  0  0  0  0  0999 V2000
   -6.2188    0.5436   -2.8321 N   0  0  0  0  0  0  0  0  0  0  0  0
   -5.7263    0.2286   -1.6573 C   0  0  0  0  0  0  0  0  0  0  0  0
   -6.5110   -0.2224   -0.6607 N   0  0  0  0  0  0  0  0  0  0  0  0
   -6.0816   -0.5602    0.5538 C   0  0  0  0  0  0  0  0  0  0  0  0
   -6.9248   -1.0241    1.5624 O   0  0  0  0  0  0  0  0  0  0  0  0
   -4.7338   -0.4443    0.8244 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.9944   -0.6933    1.9142 N   0  0  0  0  0  0  0  0  0  0  0  0
   -2.7166   -0.3983    1.6135 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5887   -0.4931    2.4177 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.6698    0.0315    0.3414 N   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4905    0.4539   -0.3877 C   0  0  1  0  0  0  0  0  0  0  0  0
   -0.7613    1.5725    0.3164 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.6162    1.4691   -0.3516 C   0  0  2  0  0  0  0  0  0  0  0  0
    0.6802    2.2665   -1.4887 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.6819    0.0221   -0.6929 C   0  0  1  0  0  0  0  0  0  0  0  0
    1.7770   -0.6830    0.1020 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.9861   -0.0342   -0.1430 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.2653   -0.7243    0.6804 P   0  0  0  0  0  5  0  0  0  0  0  0
    3.8052   -1.5767    1.8518 O   0  0  0  0  0  0  0  0  0  0  0  0
    5.2069    0.5303    1.3276 O   0  0  0  0  0  0  0  0  0  0  0  0
    5.2497   -1.6725   -0.3169 O   0  0  0  0  0  0  0  0  0  0  0  0
    6.5889   -0.8047   -0.8719 P   0  0  0  0  0  5  0  0  0  0  0  0
    6.1997    0.0495   -2.0721 O   0  0  0  0  0  0  0  0  0  0  0  0
    7.8011   -1.8653   -1.3942 O   0  0  0  0  0  0  0  0  0  0  0  0
    7.2083    0.1439    0.3794 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5466   -0.5467   -0.5151 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.9189    0.0204   -0.1996 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.4109    0.3461   -1.4064 N   0  0  0  0  0  0  0  0  0  0  0  0
   -7.2482    0.4260   -2.9516 H   0  0  0  0  0  0  0  0  0  0  0  0
   -6.7285   -1.9392    1.9516 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5257    0.0827    3.2684 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7432    0.8229   -1.3994 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5795    1.3454    1.3865 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2180    2.5613    0.1467 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.4040    1.7762    0.3760 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.4372    1.9052   -2.0381 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.9589   -0.0648   -1.7795 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.5435   -0.5467    1.1792 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.8087   -1.7603   -0.1487 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.1585    1.2908    0.6684 H   0  0  0  0  0  0  0  0  0  0  0  0
    7.5147   -2.7978   -1.2131 H   0  0  0  0  0  0  0  0  0  0  0  0
    8.1746    0.2770    0.3043 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.7297    0.6863   -2.1173 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  2  3
  2  3  1  0
  3  4  2  0
  4  5  1  0
  4  6  1  0
  6  7  1  0
  7  8  2  0
  8  9  1  0
  8 10  1  0
 10 11  1  0
 11 12  1  0
 12 13  1  0
 13 14  1  0
 13 15  1  0
 15 16  1  0
 16 17  1  0
 17 18  1  0
 18 19  2  0
 18 20  1  0
 18 21  1  0
 21 22  1  0
 22 23  2  0
 22 24  1  0
 22 25  1  0
 15 26  1  0
 10 27  1  0
 27 28  1  0
 28  2  1  0
 27  6  2  0
 26 11  1  0
  1 29  1  0
  5 30  1  0
  9 31  1  0
 11 32  1  6
 12 33  1  0
 12 34  1  0
 13 35  1  1
 14 36  1  0
 15 37  1  6
 16 38  1  0
 16 39  1  0
 20 40  1  0
 24 41  1  0
 25 42  1  0
 28 43  1  0
M  END

HEADER    PROTEIN                                 30-OCT-12   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   30-OCT-12         0                                  
HETATM    1  C   UNK     0      -2.208  -4.489   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0      -0.268  -7.970   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0      -2.208  -6.029   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0      -0.744  -6.505   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0      -0.744  -4.013   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       1.197  -0.533   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0       1.197  -2.073   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0       2.530   0.237   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0       3.864  -2.073   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0      -1.173  -1.303   0.000  0.00  0.00           C+0
HETATM   11  N   UNK     0       5.198  -2.843   0.000  0.00  0.00           N+0
HETATM   12  N   UNK     0      -0.268  -0.057   0.000  0.00  0.00           N+0
HETATM   13  N   UNK     0       2.530  -2.843   0.000  0.00  0.00           N+0
HETATM   14  N   UNK     0       3.864  -0.533   0.000  0.00  0.00           N+0
HETATM   15  N   UNK     0      -0.268  -2.549   0.000  0.00  0.00           N+0
HETATM   16  O   UNK     0      -3.454  -6.934   0.000  0.00  0.00           O+0
HETATM   17  O   UNK     0       2.530   1.777   0.000  0.00  0.00           O+0
HETATM   18  O   UNK     0      -2.713  -1.303   0.000  0.00  0.00           O+0
HETATM   19  O   UNK     0       5.203 -11.859   0.000  0.00  0.00           O+0
HETATM   20  O   UNK     0       3.376 -13.046   0.000  0.00  0.00           O+0
HETATM   21  O   UNK     0       4.017 -10.033   0.000  0.00  0.00           O+0
HETATM   22  O   UNK     0       0.250 -10.230   0.000  0.00  0.00           O+0
HETATM   23  O   UNK     0       3.179  -9.279   0.000  0.00  0.00           O+0
HETATM   24  O   UNK     0       1.239  -8.290   0.000  0.00  0.00           O+0
HETATM   25  O   UNK     0       0.161  -5.259   0.000  0.00  0.00           O+0
HETATM   26  O   UNK     0       2.190 -11.219   0.000  0.00  0.00           O+0
HETATM   27  P   UNK     0       3.697 -11.539   0.000  0.00  0.00           P+0
HETATM   28  P   UNK     0       1.714  -9.755   0.000  0.00  0.00           P+0
HETATM   29  H   UNK     0      -3.580  -5.330   0.000  0.00  0.00           H+0
HETATM   30  H   UNK     0      -1.833  -7.594   0.000  0.00  0.00           H+0
HETATM   31  H   UNK     0      -1.833  -2.924   0.000  0.00  0.00           H+0
CONECT    1    3    5                                                       
CONECT    2    4   24                                                       
CONECT    3    1    4   16   29                                             
CONECT    4    2    3   25   30                                             
CONECT    5    1   15   25   31                                             
CONECT    6    7    8   12                                                  
CONECT    7    6   13   15                                                  
CONECT    8    6   14   17                                                  
CONECT    9   11   13   14                                                  
CONECT   10   12   15   18                                                  
CONECT   11    9                                                            
CONECT   12    6   10                                                       
CONECT   13    7    9                                                       
CONECT   14    8    9                                                       
CONECT   15    5    7   10                                                  
CONECT   16    3                                                            
CONECT   17    8                                                            
CONECT   18   10                                                            
CONECT   19   27                                                            
CONECT   20   27                                                            
CONECT   21   27                                                            
CONECT   22   28                                                            
CONECT   23   28                                                            
CONECT   24    2   28                                                       
CONECT   25    4    5                                                       
CONECT   26   27   28                                                       
CONECT   27   19   20   21   26                                             
CONECT   28   22   23   24   26                                             
CONECT   29    3                                                            
CONECT   30    4                                                            
CONECT   31    5                                                            
MASTER        0    0    0    0    0    0    0    0   31    0   66    0
END

COMPND    HMDB0059648
HETATM    1  N1  UNL     1      -6.219   0.544  -2.832  1.00  0.00           N  
HETATM    2  C1  UNL     1      -5.726   0.229  -1.657  1.00  0.00           C  
HETATM    3  N2  UNL     1      -6.511  -0.222  -0.661  1.00  0.00           N  
HETATM    4  C2  UNL     1      -6.082  -0.560   0.554  1.00  0.00           C  
HETATM    5  O1  UNL     1      -6.925  -1.024   1.562  1.00  0.00           O  
HETATM    6  C3  UNL     1      -4.734  -0.444   0.824  1.00  0.00           C  
HETATM    7  N3  UNL     1      -3.994  -0.693   1.914  1.00  0.00           N  
HETATM    8  C4  UNL     1      -2.717  -0.398   1.614  1.00  0.00           C  
HETATM    9  O2  UNL     1      -1.589  -0.493   2.418  1.00  0.00           O  
HETATM   10  N4  UNL     1      -2.670   0.031   0.341  1.00  0.00           N  
HETATM   11  C5  UNL     1      -1.491   0.454  -0.388  1.00  0.00           C  
HETATM   12  C6  UNL     1      -0.761   1.572   0.316  1.00  0.00           C  
HETATM   13  C7  UNL     1       0.616   1.469  -0.352  1.00  0.00           C  
HETATM   14  O3  UNL     1       0.680   2.267  -1.489  1.00  0.00           O  
HETATM   15  C8  UNL     1       0.682   0.022  -0.693  1.00  0.00           C  
HETATM   16  C9  UNL     1       1.777  -0.683   0.102  1.00  0.00           C  
HETATM   17  O4  UNL     1       2.986  -0.034  -0.143  1.00  0.00           O  
HETATM   18  P1  UNL     1       4.265  -0.724   0.680  1.00  0.00           P  
HETATM   19  O5  UNL     1       3.805  -1.577   1.852  1.00  0.00           O  
HETATM   20  O6  UNL     1       5.207   0.530   1.328  1.00  0.00           O  
HETATM   21  O7  UNL     1       5.250  -1.672  -0.317  1.00  0.00           O  
HETATM   22  P2  UNL     1       6.589  -0.805  -0.872  1.00  0.00           P  
HETATM   23  O8  UNL     1       6.200   0.050  -2.072  1.00  0.00           O  
HETATM   24  O9  UNL     1       7.801  -1.865  -1.394  1.00  0.00           O  
HETATM   25  O10 UNL     1       7.208   0.144   0.379  1.00  0.00           O  
HETATM   26  O11 UNL     1      -0.547  -0.547  -0.515  1.00  0.00           O  
HETATM   27  C10 UNL     1      -3.919   0.020  -0.200  1.00  0.00           C  
HETATM   28  N5  UNL     1      -4.411   0.346  -1.406  1.00  0.00           N  
HETATM   29  H1  UNL     1      -7.248   0.426  -2.952  1.00  0.00           H  
HETATM   30  H2  UNL     1      -6.728  -1.939   1.952  1.00  0.00           H  
HETATM   31  H3  UNL     1      -1.526   0.083   3.268  1.00  0.00           H  
HETATM   32  H4  UNL     1      -1.743   0.823  -1.399  1.00  0.00           H  
HETATM   33  H5  UNL     1      -0.579   1.345   1.386  1.00  0.00           H  
HETATM   34  H6  UNL     1      -1.218   2.561   0.147  1.00  0.00           H  
HETATM   35  H7  UNL     1       1.404   1.776   0.376  1.00  0.00           H  
HETATM   36  H8  UNL     1       1.437   1.905  -2.038  1.00  0.00           H  
HETATM   37  H9  UNL     1       0.959  -0.065  -1.779  1.00  0.00           H  
HETATM   38  H10 UNL     1       1.544  -0.547   1.179  1.00  0.00           H  
HETATM   39  H11 UNL     1       1.809  -1.760  -0.149  1.00  0.00           H  
HETATM   40  H12 UNL     1       5.159   1.291   0.668  1.00  0.00           H  
HETATM   41  H13 UNL     1       7.515  -2.798  -1.213  1.00  0.00           H  
HETATM   42  H14 UNL     1       8.175   0.277   0.304  1.00  0.00           H  
HETATM   43  H15 UNL     1      -3.730   0.686  -2.117  1.00  0.00           H  
CONECT    1    2    2   29
CONECT    2    3   28
CONECT    3    4    4
CONECT    4    5    6
CONECT    5   30
CONECT    6    7   27   27
CONECT    7    8    8
CONECT    8    9   10
CONECT    9   31
CONECT   10   11   27
CONECT   11   12   26   32
CONECT   12   13   33   34
CONECT   13   14   15   35
CONECT   14   36
CONECT   15   16   26   37
CONECT   16   17   38   39
CONECT   17   18
CONECT   18   19   19   20   21
CONECT   20   40
CONECT   21   22
CONECT   22   23   23   24   25
CONECT   24   41
CONECT   25   42
CONECT   27   28
CONECT   28   43
END

HMDB0059648
     RDKit          3D
8-oxo-dGDP
 43 45  0  0  0  0  0  0  0  0999 V2000
   -6.2188    0.5436   -2.8321 N   0  0  0  0  0  0  0  0  0  0  0  0
   -5.7263    0.2286   -1.6573 C   0  0  0  0  0  0  0  0  0  0  0  0
   -6.5110   -0.2224   -0.6607 N   0  0  0  0  0  0  0  0  0  0  0  0
   -6.0816   -0.5602    0.5538 C   0  0  0  0  0  0  0  0  0  0  0  0
   -6.9248   -1.0241    1.5624 O   0  0  0  0  0  0  0  0  0  0  0  0
   -4.7338   -0.4443    0.8244 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.9944   -0.6933    1.9142 N   0  0  0  0  0  0  0  0  0  0  0  0
   -2.7166   -0.3983    1.6135 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5887   -0.4931    2.4177 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.6698    0.0315    0.3414 N   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4905    0.4539   -0.3877 C   0  0  1  0  0  0  0  0  0  0  0  0
   -0.7613    1.5725    0.3164 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.6162    1.4691   -0.3516 C   0  0  2  0  0  0  0  0  0  0  0  0
    0.6802    2.2665   -1.4887 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.6819    0.0221   -0.6929 C   0  0  1  0  0  0  0  0  0  0  0  0
    1.7770   -0.6830    0.1020 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.9861   -0.0342   -0.1430 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.2653   -0.7243    0.6804 P   0  0  0  0  0  5  0  0  0  0  0  0
    3.8052   -1.5767    1.8518 O   0  0  0  0  0  0  0  0  0  0  0  0
    5.2069    0.5303    1.3276 O   0  0  0  0  0  0  0  0  0  0  0  0
    5.2497   -1.6725   -0.3169 O   0  0  0  0  0  0  0  0  0  0  0  0
    6.5889   -0.8047   -0.8719 P   0  0  0  0  0  5  0  0  0  0  0  0
    6.1997    0.0495   -2.0721 O   0  0  0  0  0  0  0  0  0  0  0  0
    7.8011   -1.8653   -1.3942 O   0  0  0  0  0  0  0  0  0  0  0  0
    7.2083    0.1439    0.3794 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5466   -0.5467   -0.5151 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.9189    0.0204   -0.1996 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.4109    0.3461   -1.4064 N   0  0  0  0  0  0  0  0  0  0  0  0
   -7.2482    0.4260   -2.9516 H   0  0  0  0  0  0  0  0  0  0  0  0
   -6.7285   -1.9392    1.9516 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5257    0.0827    3.2684 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7432    0.8229   -1.3994 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5795    1.3454    1.3865 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2180    2.5613    0.1467 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.4040    1.7762    0.3760 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.4372    1.9052   -2.0381 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.9589   -0.0648   -1.7795 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.5435   -0.5467    1.1792 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.8087   -1.7603   -0.1487 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.1585    1.2908    0.6684 H   0  0  0  0  0  0  0  0  0  0  0  0
    7.5147   -2.7978   -1.2131 H   0  0  0  0  0  0  0  0  0  0  0  0
    8.1746    0.2770    0.3043 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.7297    0.6863   -2.1173 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  2  3
  2  3  1  0
  3  4  2  0
  4  5  1  0
  4  6  1  0
  6  7  1  0
  7  8  2  0
  8  9  1  0
  8 10  1  0
 10 11  1  0
 11 12  1  0
 12 13  1  0
 13 14  1  0
 13 15  1  0
 15 16  1  0
 16 17  1  0
 17 18  1  0
 18 19  2  0
 18 20  1  0
 18 21  1  0
 21 22  1  0
 22 23  2  0
 22 24  1  0
 22 25  1  0
 15 26  1  0
 10 27  1  0
 27 28  1  0
 28  2  1  0
 27  6  2  0
 26 11  1  0
  1 29  1  0
  5 30  1  0
  9 31  1  0
 11 32  1  6
 12 33  1  0
 12 34  1  0
 13 35  1  1
 14 36  1  0
 15 37  1  6
 16 38  1  0
 16 39  1  0
 20 40  1  0
 24 41  1  0
 25 42  1  0
 28 43  1  0
M  END

Synonyms

Value	Source
2'-Deoxy-8-oxo-guanosine-5'-diphosphate	ChEBI
8-oxo-2'-Deoxyguanosine-5'-diphosphate	ChEBI
8-Oxodeoxyguanosine diphosphate	ChEBI
2'-Deoxy-8-oxo-guanosine-5'-diphosphoric acid	Generator
8-oxo-2'-Deoxyguanosine-5'-diphosphoric acid	Generator
8-Oxodeoxyguanosine diphosphoric acid	Generator
2'-Deoxy-7,8-dihydro-8-oxoguanosine diphosphate	HMDB
8-oxo-7,8-Dihydrodeoxyguanosine diphosphate	HMDB

Molecular Formula

C₁₀H₁₅N₅O₁₁P₂

Average Mass

443.2005

Monoisotopic Mass

443.024329371

IUPAC Name

[({[(2R,3S,5R)-5-(6,8-dihydroxy-2-imino-3,9-dihydro-2H-purin-9-yl)-3-hydroxyoxolan-2-yl]methoxy}(hydroxy)phosphoryl)oxy]phosphonic acid

Traditional Name

{[(2R,3S,5R)-5-(6,8-dihydroxy-2-imino-3H-purin-9-yl)-3-hydroxyoxolan-2-yl]methoxy(hydroxy)phosphoryl}oxyphosphonic acid

CAS Registry Number

Not Available

SMILES

[H][C@]1(O)C[C@@]([H])(O[C@]1([H])COP(O)(=O)OP(O)(O)=O)N1C(O)=NC2=C1NC(=N)N=C2O

InChI Identifier

InChI=1S/C10H15N5O11P2/c11-9-13-7-6(8(17)14-9)12-10(18)15(7)5-1-3(16)4(25-5)2-24-28(22,23)26-27(19,20)21/h3-5,16H,1-2H2,(H,12,18)(H,22,23)(H2,19,20,21)(H3,11,13,14,17)/t3-,4+,5+/m0/s1

InChI Key

LJMLTZSNWOCYNQ-VPENINKCSA-N

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as purine 2'-deoxyribonucleoside diphosphates. These are purine nucleotides with diphosphate group linked to the ribose moiety lacking a hydroxyl group at position 2.

Kingdom

Organic compounds

Super Class

Nucleosides, nucleotides, and analogues

Class

Purine nucleotides

Sub Class

Purine deoxyribonucleotides

Direct Parent

Purine 2'-deoxyribonucleoside diphosphates

Alternative Parents

Substituents

Purine 2'-deoxyribonucleoside diphosphate
6-oxopurine
Hypoxanthine
Organic pyrophosphate
Purinone
Imidazopyrimidine
Purine
Aminopyrimidine
Pyrimidone
Monoalkyl phosphate
N-substituted imidazole
Organic phosphoric acid derivative
Phosphoric acid ester
Pyrimidine
Alkyl phosphate
Vinylogous amide
Heteroaromatic compound
Tetrahydrofuran
Azole
Imidazole
Urea
Secondary alcohol
Organoheterocyclic compound
Azacycle
Oxacycle
Organic oxygen compound
Alcohol
Organic nitrogen compound
Organic oxide
Hydrocarbon derivative
Organopnictogen compound
Organonitrogen compound
Organooxygen compound
Amine
Primary amine
Aromatic heteropolycyclic compound

Molecular Framework

Aromatic heteropolycyclic compounds

External Descriptors

purine 2'-deoxyribonucleoside 5'-diphosphate (CHEBI:63728 )

Functional Ontology

Not Available

Physical Properties

State

Expected Solid

Predicted Properties

Property	Value	Source
Water Solubility	5.62 g/L	ALOGPS
logP	-1.4	ALOGPS
logP	-1.9	ChemAxon
logS	-1.9	ALOGPS
pKa (Strongest Acidic)	1.77	ChemAxon
pKa (Strongest Basic)	5.36	ChemAxon
Physiological Charge	-3	ChemAxon
Hydrogen Acceptor Count	13	ChemAxon
Hydrogen Donor Count	8	ChemAxon
Polar Surface Area	249.27 Å²	ChemAxon
Rotatable Bond Count	6	ChemAxon
Refractivity	96.89 m³·mol⁻¹	ChemAxon
Polarizability	34.87 Å³	ChemAxon
Number of Rings	3	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 (Non-derivatized) - 70eV, Positive	splash10-004m-7930200000-a20fb46e4b0dfc26d46a	2017-09-20	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (3 TMS) - 70eV, Positive	splash10-002g-4901156000-79adcff864fe325ef3a5	2017-10-06	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (Non-derivatized) - 70eV, Positive	Not Available	2021-10-12	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (Non-derivatized) - 70eV, Positive	Not Available	2021-10-12	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Positive	splash10-014i-0900000000-dd21ac66e0afff9fd3e4	2017-10-06	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Positive	splash10-014i-0900000000-3498722a1d6b2d20b145	2017-10-06	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Positive	splash10-0gb9-0900000000-6aa657b61b284a9abf18	2017-10-06	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Negative	splash10-0006-0402900000-09beb1c445b1f9952602	2017-10-06	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Negative	splash10-01t9-9800000000-6aa7a6b800a404e05da3	2017-10-06	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Negative	splash10-004i-9100000000-cffe9f9d8069f49a98be	2017-10-06	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Positive	splash10-0006-0011900000-a1df22f588122cf0a02f	2021-09-22	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Positive	splash10-014i-0911000000-23a51630e02fe757d4d2	2021-09-22	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Positive	splash10-00kb-4920000000-e8a2918c845c2ddd767a	2021-09-22	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Negative	splash10-0006-0002900000-abf50a0bdaaf3b7a4257	2021-09-23	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Negative	splash10-004i-9001200000-0f87d5142dd440caa366	2021-09-23	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Negative	splash10-004i-9001000000-e2bbfd84afcaffe485e4	2021-09-23	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 100 MHz, D₂O, predicted)		2021-09-24	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 100 MHz, D₂O, predicted)		2021-09-24	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 1000 MHz, D₂O, predicted)		2021-09-24	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 1000 MHz, D₂O, predicted)		2021-09-24	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 200 MHz, D₂O, predicted)		2021-09-24	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 200 MHz, D₂O, predicted)		2021-09-24	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 300 MHz, D₂O, predicted)		2021-09-24	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 300 MHz, D₂O, predicted)		2021-09-24	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 400 MHz, D₂O, predicted)		2021-09-24	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 400 MHz, D₂O, predicted)		2021-09-24	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 500 MHz, D₂O, predicted)		2021-09-24	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 500 MHz, D₂O, predicted)		2021-09-24	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 600 MHz, D₂O, predicted)		2021-09-24	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 600 MHz, D₂O, predicted)		2021-09-24	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 700 MHz, D₂O, predicted)		2021-09-24	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 700 MHz, D₂O, predicted)		2021-09-24	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 800 MHz, D₂O, predicted)		2021-09-24	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 800 MHz, D₂O, predicted)		2021-09-24	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 900 MHz, D₂O, predicted)		2021-09-24	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 900 MHz, D₂O, predicted)		2021-09-24	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
MMDBp0192269	ADP-sugar pyrophosphatase	Unknown	Q9UKK9	Homo sapiens
MMDBp0195546	8-oxo-dGDP phosphatase NUDT18	Unknown	Q6ZVK8	Homo sapiens

Human Pathways

Pathways

Name	SMPDB/PathBank

Metabolic Reactions

Reaction ID	Precursor	Product	Enzyme	Reaction Type	Data Source	Reference
MMDBr0015111	8-oxo-dGDP	8-oxo-dGMP	ADP-ribose pyrophosphatase	Dephosphorylation	RHEA	34755880
MMDBr0017035	8-oxo-dGTP	8-oxo-dGDP	8-oxo-(d)GTP phosphatase	Dephosphorylation	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	Actinobacteria	3	Human
Bacteria	Proteobacteria	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

HMDB0059648

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

C20176

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

49835950

PDB ID

8GD

ChEBI ID

63728

Food Biomarker Ontology

Not Available

References

Synthesis Reference

Not Available

General References

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 8-oxo-dGDP (MMDBc0054308)

MOL for #<Metabolite:0x00007fa4ec57d080>

3D MOL for #<Metabolite:0x00007fa4ec57d080>

3D SDF for #<Metabolite:0x00007fa4ec57d080>

3D-SDF for #<Metabolite:0x00007fa4ec57d080>

PDB for #<Metabolite:0x00007fa4ec57d080>

3D PDB for #<Metabolite:0x00007fa4ec57d080>

SMILES for #<Metabolite:0x00007fa4ec57d080>

INCHI for #<Metabolite:0x00007fa4ec57d080>

Structure for #<Metabolite:0x00007fa4ec57d080>

3D Structure for #<Metabolite:0x00007fa4ec57d080>