MiMeDB: Showing metabocard for 8-oxo-dGMP (MMDBc0031161)

Record Information

Version

1.0

Status

Detected and Quantified

Creation Date

2021-11-18 00:37:49 UTC

Update Date

2024-10-15 18:10:25 UTC

Metabolite ID

MMDBc0031161

Metabolite Identification

Common Name

8-oxo-dGMP

Description

8-Oxo-dGMP is a metabolite of 8-oxo-dGTP which is a potent mutagenic substrate for DNA synthesis. 8-Oxo-dGTP is rapidly degraded to 8-oxo-dGMP by cellular 8-oxo-dGTPase activity.

Structure

MOL SDF PDB SMILES InChI


  Mrv1652304202017232D          

 24 26  0  0  1  0            999 V2000
 9673.2399 9666.4312    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
 9672.5882 9666.8919    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
 9673.9994 9666.9964    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
 9673.3225 9665.5564    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
 9672.8834 9667.7487    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
 9673.7725 9667.7451    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
 9674.7732 9666.6508    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
 9674.1397 9665.2002    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
 9674.8704 9665.7366    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
 9675.4572 9667.1620    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
 9674.2334 9664.3470    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
 9672.3853 9668.4501    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
 9669.5968 9666.9351    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
 9668.9056 9666.5361    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
 9668.2144 9666.9350    0.0000 P   0  0  0  0  0  0  0  0  0  0  0  0
 9668.6126 9667.6251    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
 9667.5193 9666.5341    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
 9667.8143 9667.6251    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
 9671.1001 9667.1129    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
 9670.4545 9666.6438    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
 9670.7011 9665.8848    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
 9671.4992 9665.8848    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
 9671.7457 9666.6438    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
 9670.2319 9665.2392    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
  2  5  1  0  0  0  0
  3  6  1  0  0  0  0
  3  7  1  0  0  0  0
  4  8  2  0  0  0  0
  7  9  1  0  0  0  0
  7 10  2  0  0  0  0
  8 11  1  0  0  0  0
  5  6  1  0  0  0  0
  8  9  1  0  0  0  0
  5 12  2  0  0  0  0
 14 15  1  0  0  0  0
 15 16  2  0  0  0  0
 15 17  1  0  0  0  0
 15 18  1  0  0  0  0
 14 13  1  0  0  0  0
 20 21  1  0  0  0  0
 21 22  1  0  0  0  0
 22 23  1  0  0  0  0
 19 20  1  0  0  0  0
 19 23  1  0  0  0  0
 23  2  1  1  0  0  0
 20 13  1  1  0  0  0
 21 24  1  6  0  0  0
M  END
> <DATABASE_ID>
MMDBc0031161

> <DATABASE_NAME>
MIME

> <SMILES>
NC1=NC2=C(NC(=O)N2[C@H]2C[C@H](O)[C@@H](COP(O)(O)=O)O2)C(=O)N1

> <INCHI_IDENTIFIER>
InChI=1S/C10H14N5O8P/c11-9-13-7-6(8(17)14-9)12-10(18)15(7)5-1-3(16)4(23-5)2-22-24(19,20)21/h3-5,16H,1-2H2,(H,12,18)(H2,19,20,21)(H3,11,13,14,17)/t3-,4+,5+/m0/s1

> <INCHI_KEY>
AQIVLFLYHYFRKU-VPENINKCSA-N

> <FORMULA>
C10H14N5O8P

> <MOLECULAR_WEIGHT>
363.2206

> <EXACT_MASS>
363.057998961

> <JCHEM_ACCEPTOR_COUNT>
11

> <JCHEM_ATOM_COUNT>
38

> <JCHEM_AVERAGE_POLARIZABILITY>
30.457682069874423

> <JCHEM_BIOAVAILABILITY>
0

> <JCHEM_DONOR_COUNT>
7

> <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}phosphonic acid

> <ALOGPS_LOGP>
-1.77

> <JCHEM_LOGP>
-1.14326113962934

> <ALOGPS_LOGS>
-1.74

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
3

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-2

> <JCHEM_PKA>
6.246768377936768

> <JCHEM_PKA_STRONGEST_ACIDIC>
1.2901356699285325

> <JCHEM_PKA_STRONGEST_BASIC>
0.33016240569988653

> <JCHEM_POLAR_SURFACE_AREA>
202.73999999999998

> <JCHEM_REFRACTIVITY>
86.01859999999999

> <JCHEM_ROTATABLE_BOND_COUNT>
4

> <JCHEM_RULE_OF_FIVE>
0

> <ALOGPS_SOLUBILITY>
6.61e+00 g/l

> <JCHEM_TRADITIONAL_IUPAC>
[(2R,3S,5R)-5-(6,8-dihydroxy-2-imino-3H-purin-9-yl)-3-hydroxyoxolan-2-yl]methoxyphosphonic acid

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 20-APR-20   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   20-APR-20         0                                  
HETATM    1  C   UNK     0    8056.7148044.005   0.000  0.00  0.00           C+0
HETATM    2  N   UNK     0    8055.4988044.865   0.000  0.00  0.00           N+0
HETATM    3  C   UNK     0    8058.1328045.060   0.000  0.00  0.00           C+0
HETATM    4  N   UNK     0    8056.8698042.372   0.000  0.00  0.00           N+0
HETATM    5  C   UNK     0    8056.0498046.464   0.000  0.00  0.00           C+0
HETATM    6  N   UNK     0    8057.7098046.457   0.000  0.00  0.00           N+0
HETATM    7  C   UNK     0    8059.5778044.415   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0    8058.3948041.707   0.000  0.00  0.00           C+0
HETATM    9  N   UNK     0    8059.7588042.708   0.000  0.00  0.00           N+0
HETATM   10  O   UNK     0    8060.8548045.369   0.000  0.00  0.00           O+0
HETATM   11  N   UNK     0    8058.5698040.114   0.000  0.00  0.00           N+0
HETATM   12  O   UNK     0    8055.1198047.773   0.000  0.00  0.00           O+0
HETATM   13  C   UNK     0    8049.9148044.946   0.000  0.00  0.00           C+0
HETATM   14  O   UNK     0    8048.6248044.201   0.000  0.00  0.00           O+0
HETATM   15  P   UNK     0    8047.3348044.945   0.000  0.00  0.00           P+0
HETATM   16  O   UNK     0    8048.0778046.234   0.000  0.00  0.00           O+0
HETATM   17  O   UNK     0    8046.0368044.197   0.000  0.00  0.00           O+0
HETATM   18  O   UNK     0    8046.5878046.234   0.000  0.00  0.00           O+0
HETATM   19  O   UNK     0    8052.7208045.277   0.000  0.00  0.00           O+0
HETATM   20  C   UNK     0    8051.5158044.402   0.000  0.00  0.00           C+0
HETATM   21  C   UNK     0    8051.9758042.985   0.000  0.00  0.00           C+0
HETATM   22  C   UNK     0    8053.4658042.985   0.000  0.00  0.00           C+0
HETATM   23  C   UNK     0    8053.9258044.402   0.000  0.00  0.00           C+0
HETATM   24  O   UNK     0    8051.1008041.780   0.000  0.00  0.00           O+0
CONECT    1    2    3    4                                                  
CONECT    2    1    5   23                                                  
CONECT    3    1    6    7                                                  
CONECT    4    1    8                                                       
CONECT    5    2    6   12                                                  
CONECT    6    3    5                                                       
CONECT    7    3    9   10                                                  
CONECT    8    4   11    9                                                  
CONECT    9    7    8                                                       
CONECT   10    7                                                            
CONECT   11    8                                                            
CONECT   12    5                                                            
CONECT   13   14   20                                                       
CONECT   14   15   13                                                       
CONECT   15   14   16   17   18                                             
CONECT   16   15                                                            
CONECT   17   15                                                            
CONECT   18   15                                                            
CONECT   19   20   23                                                       
CONECT   20   21   19   13                                                  
CONECT   21   20   22   24                                                  
CONECT   22   21   23                                                       
CONECT   23   22   19    2                                                  
CONECT   24   21                                                            
MASTER        0    0    0    0    0    0    0    0   24    0   52    0
END

Synonyms

Value	Source
2'-Deoxy-7,8-dihydro-8-oxo-5'-guanylic acid	ChEBI
2'-Deoxy-7,8-dihydro-8-oxoguanosine 5'-monophosphate	ChEBI
8-Hydroxydeoxyguanosine 5'-monophosphate	ChEBI
8-OH-dGMP	ChEBI
8-oxo-2'-Deoxyguanosine-5'-monophosphate	ChEBI
2'-Deoxy-7,8-dihydro-8-oxo-5'-guanylate	Kegg
2'-Deoxy-7,8-dihydro-8-oxoguanosine 5'-monophosphoric acid	Generator
8-Hydroxydeoxyguanosine 5'-monophosphoric acid	Generator
8-oxo-2'-Deoxyguanosine-5'-monophosphoric acid	Generator

Molecular Formula

C₁₀H₁₄N₅O₈P

Average Mass

363.2206

Monoisotopic Mass

363.057998961

IUPAC Name

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

Traditional Name

[(2R,3S,5R)-5-(6,8-dihydroxy-2-imino-3H-purin-9-yl)-3-hydroxyoxolan-2-yl]methoxyphosphonic acid

CAS Registry Number

Not Available

SMILES

NC1=NC2=C(NC(=O)N2[C@H]2C[C@H](O)[C@@H](COP(O)(O)=O)O2)C(=O)N1

InChI Identifier

InChI=1S/C10H14N5O8P/c11-9-13-7-6(8(17)14-9)12-10(18)15(7)5-1-3(16)4(23-5)2-22-24(19,20)21/h3-5,16H,1-2H2,(H,12,18)(H2,19,20,21)(H3,11,13,14,17)/t3-,4+,5+/m0/s1

InChI Key

AQIVLFLYHYFRKU-VPENINKCSA-N

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as purine 2'-deoxyribonucleoside monophosphates. These are purine nucleotides with monophosphate 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 monophosphates

Alternative Parents

Substituents

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

Molecular Framework

Aromatic heteropolycyclic compounds

External Descriptors

purine 2'-deoxyribonucleoside 5'-monophosphate (CHEBI:63223 )

Functional Ontology

Not Available

Physical Properties

State

Solid

Predicted Properties

Property	Value	Source
Water Solubility	6.61 g/L	ALOGPS
logP	-1.8	ALOGPS
logP	-1.1	ChemAxon
logS	-1.7	ALOGPS
pKa (Strongest Acidic)	1.29	ChemAxon
pKa (Strongest Basic)	0.33	ChemAxon
Physiological Charge	-2	ChemAxon
Hydrogen Acceptor Count	11	ChemAxon
Hydrogen Donor Count	7	ChemAxon
Polar Surface Area	202.74 Å²	ChemAxon
Rotatable Bond Count	4	ChemAxon
Refractivity	86.02 m³·mol⁻¹	ChemAxon
Polarizability	30.46 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	No	ChemAxon

Spectra

Spectrum Type	Description	Splash Key	Deposition Date	View
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TMS_4_9) - 70eV, Positive	Not Available	2022-08-08	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Positive	splash10-014i-0900000000-42f21e68a3b8a11d8f12	2015-09-15	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Positive	splash10-014i-0900000000-de34592c0dc9520d28b9	2015-09-15	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Positive	splash10-0gb9-0900000000-0ba8f7824c370f6cc73d	2015-09-15	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Negative	splash10-03fr-5209000000-1cfe1dad9de4df88a5ac	2015-09-15	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Negative	splash10-004i-9400000000-e52ecd6c80029deb2695	2015-09-15	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Negative	splash10-004i-9100000000-9cd024afaf90bd3fd2bd	2015-09-15	View Spectrum
MS	Mass Spectrum (Electron Ionization)	Not Available	2022-08-06	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 100 MHz, H₂O, predicted)		2022-08-22	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 100 MHz, H₂O, predicted)		2022-08-22	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 1000 MHz, H₂O, predicted)		2022-08-22	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 1000 MHz, H₂O, predicted)		2022-08-22	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 200 MHz, H₂O, predicted)		2022-08-22	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 200 MHz, H₂O, predicted)		2022-08-22	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 300 MHz, H₂O, predicted)		2022-08-22	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 300 MHz, H₂O, predicted)		2022-08-22	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 400 MHz, H₂O, predicted)		2022-08-22	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 400 MHz, H₂O, predicted)		2022-08-22	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 500 MHz, H₂O, predicted)		2022-08-22	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 500 MHz, H₂O, predicted)		2022-08-22	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 600 MHz, H₂O, predicted)		2022-08-22	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 600 MHz, H₂O, predicted)		2022-08-22	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 700 MHz, H₂O, predicted)		2022-08-22	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 700 MHz, H₂O, predicted)		2022-08-22	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 800 MHz, H₂O, predicted)		2022-08-22	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 800 MHz, H₂O, predicted)		2022-08-22	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 900 MHz, H₂O, predicted)		2022-08-22	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 900 MHz, H₂O, predicted)		2022-08-22	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

Reactions

Reaction ID	Precursor	Product	Enzyme	Reaction Type	Data Source	Reference

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	5	Human ; Human feces; Human feces; pleural fluid plaque; bal; Human stool	Unknown
Bacteria	Firmicutes	4	Human feces; Human
Bacteria	Actinobacteria	3	Human
Eukaryota/Fungi	Ascomycota	2	Human feces; Human saliva	Unknown

Exposure Sources

Source Type	Source Sub-type	Species	Data Source	Reference

Host Biospecimen and Location

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

External Links

HMDB ID

Not Available

DrugBank ID

DB02023

Phenol Explorer Compound ID

Not Available

FooDB ID

Not Available

KNApSAcK ID

Not Available

Chemspider ID

Not Available

KEGG Compound ID

C19968

BioCyc ID

CPD-12365

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

447903

PDB ID

Not Available

ChEBI ID

63223

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-dGMP (MMDBc0031161)

MOL for #<Metabolite:0x00007faae9050e38>

3D MOL for #<Metabolite:0x00007faae9050e38>

3D SDF for #<Metabolite:0x00007faae9050e38>

3D-SDF for #<Metabolite:0x00007faae9050e38>

PDB for #<Metabolite:0x00007faae9050e38>

3D PDB for #<Metabolite:0x00007faae9050e38>

SMILES for #<Metabolite:0x00007faae9050e38>

INCHI for #<Metabolite:0x00007faae9050e38>

Structure for #<Metabolite:0x00007faae9050e38>

3D Structure for #<Metabolite:0x00007faae9050e38>