MiMeDB: Showing metabocard for 2'-Deoxyguanosine 5'-diphosphate (MMDBc0057194)

Record Information

Version

1.0

Status

Detected and Quantified

Creation Date

2022-11-09 20:24:52 UTC

Update Date

2022-12-15 22:52:23 UTC

Metabolite ID

MMDBc0057194

Metabolite Identification

Common Name

2'-Deoxyguanosine 5'-diphosphate

Description

dGDP, also known as 2'-deoxy-GDP or 5'-dGDP, belongs to the class of organic compounds known as hydroxycinnamic acids. Hydroxycinnamic acids are compounds containing an cinnamic acid where the benzene ring is hydroxylated. dGDP is a moderately basic compound (based on its pKa). dGDP exists in all eukaryotes, ranging from yeast to humans. Within humans, dGDP participates in a number of enzymatic reactions. In particular, dGDP can be converted into dGTP; which is mediated by the enzyme nucleoside diphosphate kinase 6. In addition, dGDP can be biosynthesized from 2'-deoxyguanosine 5'-monophosphate through its interaction with the enzyme guanylate kinase. In humans, dGDP is involved in the metabolic disorder called the gout or kelley-seegmiller syndrome pathway. Outside of the human body, dGDP has been detected, but not quantified in, several different foods, such as chinese bayberries, thistles, french plantains, nopals, and pepper (capsicum). This could make dGDP a potential biomarker for the consumption of these foods. A purine 2'-deoxyribonucleoside 5'-diphosphate having guanine as the nucleobase.

Structure

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


  Mrv1652309042000142D          

 27 29  0  0  1  0            999 V2000
    2.3016    0.0890    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.6737    0.5296    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    3.0335    0.6302    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.3814   -0.7574    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.9069    0.2799    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    1.9512    1.3588    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.8115    1.3518    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    3.7760    0.2972    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.1688   -1.1007    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.2305    0.7864    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.6503   -0.4660    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.8731   -0.5839    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    4.4351    0.7898    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.2590   -1.9230    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4251    0.3146    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
   -0.1684   -0.4660    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
   -1.2091    0.5713    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4355   -1.2465    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8301    0.0162    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.6591    0.0162    0.0000 P   0  0  0  0  0  0  0  0  0  0  0  0
   -3.4884    0.0162    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.6627   -0.8129    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.6627    0.8487    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -4.3174    0.0232    0.0000 P   0  0  0  0  0  0  0  0  0  0  0  0
   -4.3243   -0.8095    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -5.1501    0.0232    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -4.3243    0.8521    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0  0  0  0
  1  3  2  0  0  0  0
  1  4  1  0  0  0  0
  5  2  1  1  0  0  0
  2  6  1  0  0  0  0
  3  7  1  0  0  0  0
  3  8  1  0  0  0  0
  4  9  2  0  0  0  0
  5 10  1  0  0  0  0
  5 11  1  0  0  0  0
  8 12  1  0  0  0  0
  8 13  2  0  0  0  0
  9 14  1  0  0  0  0
 10 15  1  0  0  0  0
 11 16  1  0  0  0  0
 15 17  1  1  0  0  0
 16 18  1  6  0  0  0
 17 19  1  0  0  0  0
 19 20  1  0  0  0  0
 20 21  1  0  0  0  0
 20 22  1  0  0  0  0
 20 23  2  0  0  0  0
 21 24  1  0  0  0  0
 24 25  1  0  0  0  0
 24 26  1  0  0  0  0
 24 27  2  0  0  0  0
  6  7  2  0  0  0  0
  9 12  1  0  0  0  0
 15 16  1  0  0  0  0
M  END

HMDB0000960
     RDKit          3D
dGDP
 42 44  0  0  0  0  0  0  0  0999 V2000
   -4.1919    3.0542   -0.1746 N   0  0  0  0  0  0  0  0  0  0  0  0
   -4.2979    1.6654    0.0623 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.2103    0.8604    0.1651 N   0  0  0  0  0  0  0  0  0  0  0  0
   -3.4333   -0.4454    0.3916 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.7046   -0.9626    0.5168 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.5770   -2.2728    0.7335 N   0  0  0  0  0  0  0  0  0  0  0  0
   -3.2741   -2.5780    0.7457 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.5608   -1.4567    0.5356 N   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1216   -1.4347    0.4887 C   0  0  1  0  0  0  0  0  0  0  0  0
   -0.5908   -1.7624   -0.8972 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.8554   -1.2813   -0.7696 C   0  0  2  0  0  0  0  0  0  0  0  0
    1.6213   -2.4413   -0.5292 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.7720   -0.4065    0.4479 C   0  0  1  0  0  0  0  0  0  0  0  0
    1.5324    0.8890    0.2775 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.8711    0.5968    0.0214 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.7906    1.9927   -0.1816 P   0  0  0  0  0  5  0  0  0  0  0  0
    4.3538    2.3793    1.1618 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.8595    3.2486   -0.7671 O   0  0  0  0  0  0  0  0  0  0  0  0
    5.1075    1.6520   -1.1967 O   0  0  0  0  0  0  0  0  0  0  0  0
    6.2127    0.6452   -0.4526 P   0  0  0  0  0  5  0  0  0  0  0  0
    7.6279    0.8943   -0.9571 O   0  0  0  0  0  0  0  0  0  0  0  0
    6.2161    0.8171    1.2327 O   0  0  0  0  0  0  0  0  0  0  0  0
    5.8892   -1.0007   -0.7755 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5789   -0.1820    0.7071 O   0  0  0  0  0  0  0  0  0  0  0  0
   -5.7979   -0.1288    0.4093 C   0  0  0  0  0  0  0  0  0  0  0  0
   -6.9811   -0.5849    0.5216 O   0  0  0  0  0  0  0  0  0  0  0  0
   -5.5602    1.1716    0.1833 N   0  0  0  0  0  0  0  0  0  0  0  0
   -3.7036    3.6444    0.5209 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.5859    3.5016   -1.0197 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8773   -3.5876    0.9037 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6575   -2.1299    1.2308 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6358   -2.8408   -1.1254 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1160   -1.1342   -1.6420 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.1945   -0.7515   -1.6703 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.2233   -3.2226   -1.0298 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.1941   -0.9626    1.3053 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.5150    1.4995    1.1982 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.1333    1.4209   -0.6060 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.1375    3.5680   -1.6610 H   0  0  0  0  0  0  0  0  0  0  0  0
    6.5068   -0.0366    1.6766 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.2471   -1.2914   -0.0858 H   0  0  0  0  0  0  0  0  0  0  0  0
   -6.4043    1.7956    0.1037 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  2  3  2  0
  3  4  1  0
  4  5  2  0
  5  6  1  0
  6  7  2  0
  7  8  1  0
  8  9  1  0
  9 10  1  0
 10 11  1  0
 11 12  1  0
 11 13  1  0
 13 14  1  0
 14 15  1  0
 15 16  1  0
 16 17  2  0
 16 18  1  0
 16 19  1  0
 19 20  1  0
 20 21  2  0
 20 22  1  0
 20 23  1  0
 13 24  1  0
  5 25  1  0
 25 26  2  0
 25 27  1  0
 27  2  1  0
  8  4  1  0
 24  9  1  0
  1 28  1  0
  1 29  1  0
  7 30  1  0
  9 31  1  1
 10 32  1  0
 10 33  1  0
 11 34  1  6
 12 35  1  0
 13 36  1  1
 14 37  1  0
 14 38  1  0
 18 39  1  0
 22 40  1  0
 23 41  1  0
 27 42  1  0
M  END


  Mrv1652309042000142D          

 27 29  0  0  1  0            999 V2000
    2.3016    0.0890    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.6737    0.5296    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    3.0335    0.6302    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.3814   -0.7574    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.9069    0.2799    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    1.9512    1.3588    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.8115    1.3518    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    3.7760    0.2972    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.1688   -1.1007    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.2305    0.7864    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.6503   -0.4660    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.8731   -0.5839    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    4.4351    0.7898    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.2590   -1.9230    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4251    0.3146    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
   -0.1684   -0.4660    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
   -1.2091    0.5713    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4355   -1.2465    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8301    0.0162    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.6591    0.0162    0.0000 P   0  0  0  0  0  0  0  0  0  0  0  0
   -3.4884    0.0162    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.6627   -0.8129    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.6627    0.8487    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -4.3174    0.0232    0.0000 P   0  0  0  0  0  0  0  0  0  0  0  0
   -4.3243   -0.8095    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -5.1501    0.0232    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -4.3243    0.8521    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0  0  0  0
  1  3  2  0  0  0  0
  1  4  1  0  0  0  0
  5  2  1  1  0  0  0
  2  6  1  0  0  0  0
  3  7  1  0  0  0  0
  3  8  1  0  0  0  0
  4  9  2  0  0  0  0
  5 10  1  0  0  0  0
  5 11  1  0  0  0  0
  8 12  1  0  0  0  0
  8 13  2  0  0  0  0
  9 14  1  0  0  0  0
 10 15  1  0  0  0  0
 11 16  1  0  0  0  0
 15 17  1  1  0  0  0
 16 18  1  6  0  0  0
 17 19  1  0  0  0  0
 19 20  1  0  0  0  0
 20 21  1  0  0  0  0
 20 22  1  0  0  0  0
 20 23  2  0  0  0  0
 21 24  1  0  0  0  0
 24 25  1  0  0  0  0
 24 26  1  0  0  0  0
 24 27  2  0  0  0  0
  6  7  2  0  0  0  0
  9 12  1  0  0  0  0
 15 16  1  0  0  0  0
M  END
> <DATABASE_ID>
MMDBc0057194

> <DATABASE_NAME>
MIME

> <SMILES>
NC1=NC2=C(N=CN2[C@H]2C[C@H](O)[C@@H](COP(O)(=O)OP(O)(O)=O)O2)C(=O)N1

> <INCHI_IDENTIFIER>
InChI=1S/C10H15N5O10P2/c11-10-13-8-7(9(17)14-10)12-3-15(8)6-1-4(16)5(24-6)2-23-27(21,22)25-26(18,19)20/h3-6,16H,1-2H2,(H,21,22)(H2,18,19,20)(H3,11,13,14,17)/t4-,5+,6+/m0/s1

> <INCHI_KEY>
CIKGWCTVFSRMJU-KVQBGUIXSA-N

> <FORMULA>
C10H15N5O10P2

> <MOLECULAR_WEIGHT>
427.2011

> <EXACT_MASS>
427.029414749

> <JCHEM_ACCEPTOR_COUNT>
11

> <JCHEM_ATOM_COUNT>
42

> <JCHEM_AVERAGE_POLARIZABILITY>
34.98723478823068

> <JCHEM_BIOAVAILABILITY>
0

> <JCHEM_DONOR_COUNT>
6

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
[({[(2R,3S,5R)-5-(2-amino-6-oxo-6,9-dihydro-1H-purin-9-yl)-3-hydroxyoxolan-2-yl]methoxy}(hydroxy)phosphoryl)oxy]phosphonic acid

> <ALOGPS_LOGP>
-1.45

> <JCHEM_LOGP>
-2.518337817879012

> <ALOGPS_LOGS>
-2.07

> <JCHEM_MDDR_LIKE_RULE>
1

> <JCHEM_NUMBER_OF_RINGS>
3

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-2

> <JCHEM_PKA>
3.211180454774107

> <JCHEM_PKA_STRONGEST_ACIDIC>
1.791789653298578

> <JCHEM_PKA_STRONGEST_BASIC>
0.44204991344968037

> <JCHEM_POLAR_SURFACE_AREA>
228.04999999999995

> <JCHEM_REFRACTIVITY>
84.85619999999997

> <JCHEM_ROTATABLE_BOND_COUNT>
6

> <JCHEM_RULE_OF_FIVE>
0

> <ALOGPS_SOLUBILITY>
3.60e+00 g/l

> <JCHEM_TRADITIONAL_IUPAC>
dGDP

> <JCHEM_VEBER_RULE>
0

$$$$

HMDB0000960
     RDKit          3D
dGDP
 42 44  0  0  0  0  0  0  0  0999 V2000
   -4.1919    3.0542   -0.1746 N   0  0  0  0  0  0  0  0  0  0  0  0
   -4.2979    1.6654    0.0623 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.2103    0.8604    0.1651 N   0  0  0  0  0  0  0  0  0  0  0  0
   -3.4333   -0.4454    0.3916 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.7046   -0.9626    0.5168 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.5770   -2.2728    0.7335 N   0  0  0  0  0  0  0  0  0  0  0  0
   -3.2741   -2.5780    0.7457 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.5608   -1.4567    0.5356 N   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1216   -1.4347    0.4887 C   0  0  1  0  0  0  0  0  0  0  0  0
   -0.5908   -1.7624   -0.8972 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.8554   -1.2813   -0.7696 C   0  0  2  0  0  0  0  0  0  0  0  0
    1.6213   -2.4413   -0.5292 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.7720   -0.4065    0.4479 C   0  0  1  0  0  0  0  0  0  0  0  0
    1.5324    0.8890    0.2775 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.8711    0.5968    0.0214 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.7906    1.9927   -0.1816 P   0  0  0  0  0  5  0  0  0  0  0  0
    4.3538    2.3793    1.1618 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.8595    3.2486   -0.7671 O   0  0  0  0  0  0  0  0  0  0  0  0
    5.1075    1.6520   -1.1967 O   0  0  0  0  0  0  0  0  0  0  0  0
    6.2127    0.6452   -0.4526 P   0  0  0  0  0  5  0  0  0  0  0  0
    7.6279    0.8943   -0.9571 O   0  0  0  0  0  0  0  0  0  0  0  0
    6.2161    0.8171    1.2327 O   0  0  0  0  0  0  0  0  0  0  0  0
    5.8892   -1.0007   -0.7755 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5789   -0.1820    0.7071 O   0  0  0  0  0  0  0  0  0  0  0  0
   -5.7979   -0.1288    0.4093 C   0  0  0  0  0  0  0  0  0  0  0  0
   -6.9811   -0.5849    0.5216 O   0  0  0  0  0  0  0  0  0  0  0  0
   -5.5602    1.1716    0.1833 N   0  0  0  0  0  0  0  0  0  0  0  0
   -3.7036    3.6444    0.5209 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.5859    3.5016   -1.0197 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8773   -3.5876    0.9037 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6575   -2.1299    1.2308 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6358   -2.8408   -1.1254 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1160   -1.1342   -1.6420 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.1945   -0.7515   -1.6703 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.2233   -3.2226   -1.0298 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.1941   -0.9626    1.3053 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.5150    1.4995    1.1982 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.1333    1.4209   -0.6060 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.1375    3.5680   -1.6610 H   0  0  0  0  0  0  0  0  0  0  0  0
    6.5068   -0.0366    1.6766 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.2471   -1.2914   -0.0858 H   0  0  0  0  0  0  0  0  0  0  0  0
   -6.4043    1.7956    0.1037 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  2  3  2  0
  3  4  1  0
  4  5  2  0
  5  6  1  0
  6  7  2  0
  7  8  1  0
  8  9  1  0
  9 10  1  0
 10 11  1  0
 11 12  1  0
 11 13  1  0
 13 14  1  0
 14 15  1  0
 15 16  1  0
 16 17  2  0
 16 18  1  0
 16 19  1  0
 19 20  1  0
 20 21  2  0
 20 22  1  0
 20 23  1  0
 13 24  1  0
  5 25  1  0
 25 26  2  0
 25 27  1  0
 27  2  1  0
  8  4  1  0
 24  9  1  0
  1 28  1  0
  1 29  1  0
  7 30  1  0
  9 31  1  1
 10 32  1  0
 10 33  1  0
 11 34  1  6
 12 35  1  0
 13 36  1  1
 14 37  1  0
 14 38  1  0
 18 39  1  0
 22 40  1  0
 23 41  1  0
 27 42  1  0
M  END

HEADER    PROTEIN                                 04-SEP-20   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   04-SEP-20         0                                  
HETATM    1  C   UNK     0       4.296   0.166   0.000  0.00  0.00           C+0
HETATM    2  N   UNK     0       3.124   0.989   0.000  0.00  0.00           N+0
HETATM    3  C   UNK     0       5.663   1.176   0.000  0.00  0.00           C+0
HETATM    4  N   UNK     0       4.445  -1.414   0.000  0.00  0.00           N+0
HETATM    5  C   UNK     0       1.693   0.522   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       3.642   2.536   0.000  0.00  0.00           C+0
HETATM    7  N   UNK     0       5.248   2.523   0.000  0.00  0.00           N+0
HETATM    8  C   UNK     0       7.048   0.555   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0       5.915  -2.055   0.000  0.00  0.00           C+0
HETATM   10  O   UNK     0       0.430   1.468   0.000  0.00  0.00           O+0
HETATM   11  C   UNK     0       1.214  -0.870   0.000  0.00  0.00           C+0
HETATM   12  N   UNK     0       7.230  -1.090   0.000  0.00  0.00           N+0
HETATM   13  O   UNK     0       8.279   1.474   0.000  0.00  0.00           O+0
HETATM   14  N   UNK     0       6.083  -3.590   0.000  0.00  0.00           N+0
HETATM   15  C   UNK     0      -0.793   0.587   0.000  0.00  0.00           C+0
HETATM   16  C   UNK     0      -0.314  -0.870   0.000  0.00  0.00           C+0
HETATM   17  C   UNK     0      -2.257   1.066   0.000  0.00  0.00           C+0
HETATM   18  O   UNK     0      -0.813  -2.327   0.000  0.00  0.00           O+0
HETATM   19  O   UNK     0      -3.416   0.030   0.000  0.00  0.00           O+0
HETATM   20  P   UNK     0      -4.964   0.030   0.000  0.00  0.00           P+0
HETATM   21  O   UNK     0      -6.512   0.030   0.000  0.00  0.00           O+0
HETATM   22  O   UNK     0      -4.970  -1.517   0.000  0.00  0.00           O+0
HETATM   23  O   UNK     0      -4.970   1.584   0.000  0.00  0.00           O+0
HETATM   24  P   UNK     0      -8.059   0.043   0.000  0.00  0.00           P+0
HETATM   25  O   UNK     0      -8.072  -1.511   0.000  0.00  0.00           O+0
HETATM   26  O   UNK     0      -9.613   0.043   0.000  0.00  0.00           O+0
HETATM   27  O   UNK     0      -8.072   1.591   0.000  0.00  0.00           O+0
CONECT    1    2    3    4                                                  
CONECT    2    1    5    6                                                  
CONECT    3    1    7    8                                                  
CONECT    4    1    9                                                       
CONECT    5    2   10   11                                                  
CONECT    6    2    7                                                       
CONECT    7    3    6                                                       
CONECT    8    3   12   13                                                  
CONECT    9    4   14   12                                                  
CONECT   10    5   15                                                       
CONECT   11    5   16                                                       
CONECT   12    8    9                                                       
CONECT   13    8                                                            
CONECT   14    9                                                            
CONECT   15   10   17   16                                                  
CONECT   16   11   18   15                                                  
CONECT   17   15   19                                                       
CONECT   18   16                                                            
CONECT   19   17   20                                                       
CONECT   20   19   21   22   23                                             
CONECT   21   20   24                                                       
CONECT   22   20                                                            
CONECT   23   20                                                            
CONECT   24   21   25   26   27                                             
CONECT   25   24                                                            
CONECT   26   24                                                            
CONECT   27   24                                                            
MASTER        0    0    0    0    0    0    0    0   27    0   58    0
END

COMPND    HMDB0000960
HETATM    1  N1  UNL     1      -4.192   3.054  -0.175  1.00  0.00           N  
HETATM    2  C1  UNL     1      -4.298   1.665   0.062  1.00  0.00           C  
HETATM    3  N2  UNL     1      -3.210   0.860   0.165  1.00  0.00           N  
HETATM    4  C2  UNL     1      -3.433  -0.445   0.392  1.00  0.00           C  
HETATM    5  C3  UNL     1      -4.705  -0.963   0.517  1.00  0.00           C  
HETATM    6  N3  UNL     1      -4.577  -2.273   0.733  1.00  0.00           N  
HETATM    7  C4  UNL     1      -3.274  -2.578   0.746  1.00  0.00           C  
HETATM    8  N4  UNL     1      -2.561  -1.457   0.536  1.00  0.00           N  
HETATM    9  C5  UNL     1      -1.122  -1.435   0.489  1.00  0.00           C  
HETATM   10  C6  UNL     1      -0.591  -1.762  -0.897  1.00  0.00           C  
HETATM   11  C7  UNL     1       0.855  -1.281  -0.770  1.00  0.00           C  
HETATM   12  O1  UNL     1       1.621  -2.441  -0.529  1.00  0.00           O  
HETATM   13  C8  UNL     1       0.772  -0.407   0.448  1.00  0.00           C  
HETATM   14  C9  UNL     1       1.532   0.889   0.277  1.00  0.00           C  
HETATM   15  O2  UNL     1       2.871   0.597   0.021  1.00  0.00           O  
HETATM   16  P1  UNL     1       3.791   1.993  -0.182  1.00  0.00           P  
HETATM   17  O3  UNL     1       4.354   2.379   1.162  1.00  0.00           O  
HETATM   18  O4  UNL     1       2.860   3.249  -0.767  1.00  0.00           O  
HETATM   19  O5  UNL     1       5.107   1.652  -1.197  1.00  0.00           O  
HETATM   20  P2  UNL     1       6.213   0.645  -0.453  1.00  0.00           P  
HETATM   21  O6  UNL     1       7.628   0.894  -0.957  1.00  0.00           O  
HETATM   22  O7  UNL     1       6.216   0.817   1.233  1.00  0.00           O  
HETATM   23  O8  UNL     1       5.889  -1.001  -0.776  1.00  0.00           O  
HETATM   24  O9  UNL     1      -0.579  -0.182   0.707  1.00  0.00           O  
HETATM   25  C10 UNL     1      -5.798  -0.129   0.409  1.00  0.00           C  
HETATM   26  O10 UNL     1      -6.981  -0.585   0.522  1.00  0.00           O  
HETATM   27  N5  UNL     1      -5.560   1.172   0.183  1.00  0.00           N  
HETATM   28  H1  UNL     1      -3.704   3.644   0.521  1.00  0.00           H  
HETATM   29  H2  UNL     1      -4.586   3.502  -1.020  1.00  0.00           H  
HETATM   30  H3  UNL     1      -2.877  -3.588   0.904  1.00  0.00           H  
HETATM   31  H4  UNL     1      -0.658  -2.130   1.231  1.00  0.00           H  
HETATM   32  H5  UNL     1      -0.636  -2.841  -1.125  1.00  0.00           H  
HETATM   33  H6  UNL     1      -1.116  -1.134  -1.642  1.00  0.00           H  
HETATM   34  H7  UNL     1       1.195  -0.751  -1.670  1.00  0.00           H  
HETATM   35  H8  UNL     1       1.223  -3.223  -1.030  1.00  0.00           H  
HETATM   36  H9  UNL     1       1.194  -0.963   1.305  1.00  0.00           H  
HETATM   37  H10 UNL     1       1.515   1.499   1.198  1.00  0.00           H  
HETATM   38  H11 UNL     1       1.133   1.421  -0.606  1.00  0.00           H  
HETATM   39  H12 UNL     1       3.137   3.568  -1.661  1.00  0.00           H  
HETATM   40  H13 UNL     1       6.507  -0.037   1.677  1.00  0.00           H  
HETATM   41  H14 UNL     1       5.247  -1.291  -0.086  1.00  0.00           H  
HETATM   42  H15 UNL     1      -6.404   1.796   0.104  1.00  0.00           H  
CONECT    1    2   28   29
CONECT    2    3    3   27
CONECT    3    4
CONECT    4    5    5    8
CONECT    5    6   25
CONECT    6    7    7
CONECT    7    8   30
CONECT    8    9
CONECT    9   10   24   31
CONECT   10   11   32   33
CONECT   11   12   13   34
CONECT   12   35
CONECT   13   14   24   36
CONECT   14   15   37   38
CONECT   15   16
CONECT   16   17   17   18   19
CONECT   18   39
CONECT   19   20
CONECT   20   21   21   22   23
CONECT   22   40
CONECT   23   41
CONECT   25   26   26   27
CONECT   27   42
END

HMDB0000960
     RDKit          3D
dGDP
 42 44  0  0  0  0  0  0  0  0999 V2000
   -4.1919    3.0542   -0.1746 N   0  0  0  0  0  0  0  0  0  0  0  0
   -4.2979    1.6654    0.0623 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.2103    0.8604    0.1651 N   0  0  0  0  0  0  0  0  0  0  0  0
   -3.4333   -0.4454    0.3916 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.7046   -0.9626    0.5168 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.5770   -2.2728    0.7335 N   0  0  0  0  0  0  0  0  0  0  0  0
   -3.2741   -2.5780    0.7457 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.5608   -1.4567    0.5356 N   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1216   -1.4347    0.4887 C   0  0  1  0  0  0  0  0  0  0  0  0
   -0.5908   -1.7624   -0.8972 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.8554   -1.2813   -0.7696 C   0  0  2  0  0  0  0  0  0  0  0  0
    1.6213   -2.4413   -0.5292 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.7720   -0.4065    0.4479 C   0  0  1  0  0  0  0  0  0  0  0  0
    1.5324    0.8890    0.2775 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.8711    0.5968    0.0214 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.7906    1.9927   -0.1816 P   0  0  0  0  0  5  0  0  0  0  0  0
    4.3538    2.3793    1.1618 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.8595    3.2486   -0.7671 O   0  0  0  0  0  0  0  0  0  0  0  0
    5.1075    1.6520   -1.1967 O   0  0  0  0  0  0  0  0  0  0  0  0
    6.2127    0.6452   -0.4526 P   0  0  0  0  0  5  0  0  0  0  0  0
    7.6279    0.8943   -0.9571 O   0  0  0  0  0  0  0  0  0  0  0  0
    6.2161    0.8171    1.2327 O   0  0  0  0  0  0  0  0  0  0  0  0
    5.8892   -1.0007   -0.7755 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5789   -0.1820    0.7071 O   0  0  0  0  0  0  0  0  0  0  0  0
   -5.7979   -0.1288    0.4093 C   0  0  0  0  0  0  0  0  0  0  0  0
   -6.9811   -0.5849    0.5216 O   0  0  0  0  0  0  0  0  0  0  0  0
   -5.5602    1.1716    0.1833 N   0  0  0  0  0  0  0  0  0  0  0  0
   -3.7036    3.6444    0.5209 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.5859    3.5016   -1.0197 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8773   -3.5876    0.9037 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6575   -2.1299    1.2308 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6358   -2.8408   -1.1254 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1160   -1.1342   -1.6420 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.1945   -0.7515   -1.6703 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.2233   -3.2226   -1.0298 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.1941   -0.9626    1.3053 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.5150    1.4995    1.1982 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.1333    1.4209   -0.6060 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.1375    3.5680   -1.6610 H   0  0  0  0  0  0  0  0  0  0  0  0
    6.5068   -0.0366    1.6766 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.2471   -1.2914   -0.0858 H   0  0  0  0  0  0  0  0  0  0  0  0
   -6.4043    1.7956    0.1037 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  2  3  2  0
  3  4  1  0
  4  5  2  0
  5  6  1  0
  6  7  2  0
  7  8  1  0
  8  9  1  0
  9 10  1  0
 10 11  1  0
 11 12  1  0
 11 13  1  0
 13 14  1  0
 14 15  1  0
 15 16  1  0
 16 17  2  0
 16 18  1  0
 16 19  1  0
 19 20  1  0
 20 21  2  0
 20 22  1  0
 20 23  1  0
 13 24  1  0
  5 25  1  0
 25 26  2  0
 25 27  1  0
 27  2  1  0
  8  4  1  0
 24  9  1  0
  1 28  1  0
  1 29  1  0
  7 30  1  0
  9 31  1  1
 10 32  1  0
 10 33  1  0
 11 34  1  6
 12 35  1  0
 13 36  1  1
 14 37  1  0
 14 38  1  0
 18 39  1  0
 22 40  1  0
 23 41  1  0
 27 42  1  0
M  END

Synonyms

Value	Source
2'-Deoxyguanosine 5'-diphosphate	ChEBI
Deoxyguanosine diphosphate	ChEBI
2'-Deoxyguanosine 5'-diphosphoric acid	Generator
Deoxyguanosine diphosphoric acid	Generator
2'-Deoxy-GDP	HMDB
2'-Deoxyguanosine-5'-diphosphate	HMDB
5'-dGDP	HMDB
Deoxyguanosine 5'-diphosphate	HMDB
Deoxyguanosine-diphosphate	HMDB

Molecular Formula

C₁₀H₁₅N₅O₁₀P₂

Average Mass

427.2011

Monoisotopic Mass

427.029414749

IUPAC Name

[({[(2R,3S,5R)-5-(2-amino-6-oxo-6,9-dihydro-1H-purin-9-yl)-3-hydroxyoxolan-2-yl]methoxy}(hydroxy)phosphoryl)oxy]phosphonic acid

Traditional Name

dGDP

CAS Registry Number

Not Available

SMILES

NC1=NC2=C(N=CN2[C@H]2C[C@H](O)[C@@H](COP(O)(=O)OP(O)(O)=O)O2)C(=O)N1

InChI Identifier

InChI=1S/C10H15N5O10P2/c11-10-13-8-7(9(17)14-10)12-3-15(8)6-1-4(16)5(24-6)2-23-27(21,22)25-26(18,19)20/h3-6,16H,1-2H2,(H,21,22)(H2,18,19,20)(H3,11,13,14,17)/t4-,5+,6+/m0/s1

InChI Key

CIKGWCTVFSRMJU-KVQBGUIXSA-N

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as hydroxycinnamic acids. Hydroxycinnamic acids are compounds containing an cinnamic acid where the benzene ring is hydroxylated.

Kingdom

Organic compounds

Super Class

Phenylpropanoids and polyketides

Class

Cinnamic acids and derivatives

Sub Class

Hydroxycinnamic acids and derivatives

Direct Parent

Hydroxycinnamic acids

Alternative Parents

Substituents

Cinnamic acid
Coumaric acid or derivatives
Hydroxycinnamic acid
Methoxyphenol
Phenoxy compound
Anisole
Methoxybenzene
Styrene
Phenol ether
1-hydroxy-4-unsubstituted benzenoid
1-hydroxy-2-unsubstituted benzenoid
Alkyl aryl ether
Phenol
Monocyclic benzene moiety
Benzenoid
Carboxylic acid derivative
Carboxylic acid
Monocarboxylic acid or derivatives
Ether
Organic oxygen compound
Carbonyl group
Organic oxide
Organooxygen compound
Hydrocarbon derivative
Aromatic homomonocyclic compound

Molecular Framework

Aromatic homomonocyclic compounds

External Descriptors

ferulic acids (CHEBI:27794 )

Functional Ontology

Not Available

Physical Properties

State

Not Available

Predicted Properties

Property	Value	Source
Water Solubility	3.6 g/L	ALOGPS
logP	-1.4	ALOGPS
logP	-2.5	ChemAxon
logS	-2.1	ALOGPS
pKa (Strongest Acidic)	1.79	ChemAxon
pKa (Strongest Basic)	0.44	ChemAxon
Physiological Charge	-2	ChemAxon
Hydrogen Acceptor Count	11	ChemAxon
Hydrogen Donor Count	6	ChemAxon
Polar Surface Area	228.05 Å²	ChemAxon
Rotatable Bond Count	6	ChemAxon
Refractivity	84.86 m³·mol⁻¹	ChemAxon
Polarizability	34.99 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

Not Available

Biological Properties

Cellular Locations

Cytoplasm
Mitochondria
Nucleus

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

Reactions

Reaction ID	Precursor	Product	Enzyme	Reaction Type	Data Source	Reference
MMDBr0026019	2'-Deoxyguanosine 5'-monophosphate	2'-Deoxyguanosine 5'-diphosphate	Deoxynucleotide monophosphate kinase	Phosphorylation	RHEA	34755880
MMDBr0026060	L-Cystine	L-Cysteine	Vitamin B12-dependent ribonucleoside-diphosphate reductase	Reduction	RHEA	34755880
MMDBr0026088	2'-Deoxyguanosine 5'-diphosphate	2'-Deoxyguanosine 5'-triphosphate	Nucleoside diphosphate kinase	Phosphorylation	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

Exposure Sources

Other Exposures

Source Type	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

HMDB0000960

DrugBank ID

DB03491

Phenol Explorer Compound ID

Not Available

FooDB ID

KNApSAcK ID

Chemspider ID

KEGG Compound ID

BioCyc ID

BiGG ID

Wikipedia Link

Deoxyguanosine_diphosphate

METLIN ID

5906

PubChem Compound

439220

PDB ID

Not Available

ChEBI ID

28862

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 2'-Deoxyguanosine 5'-diphosphate (MMDBc0057194)

MOL for #<Metabolite:0x00005645c9bec7a0>

3D MOL for #<Metabolite:0x00005645c9bec7a0>

3D SDF for #<Metabolite:0x00005645c9bec7a0>

3D-SDF for #<Metabolite:0x00005645c9bec7a0>

PDB for #<Metabolite:0x00005645c9bec7a0>

3D PDB for #<Metabolite:0x00005645c9bec7a0>

SMILES for #<Metabolite:0x00005645c9bec7a0>

INCHI for #<Metabolite:0x00005645c9bec7a0>

Structure for #<Metabolite:0x00005645c9bec7a0>

3D Structure for #<Metabolite:0x00005645c9bec7a0>