2'-Deoxyguanosine 5'-monophosphate (ECMDB01044) (M2MDB000231)

IdentificationTaxonomyPhysical PropertiesBiological PropertiesSpectraConcentrationsLinksReferencesEnzymes (9)Transporters (4)XML
Proteins (1504)
Record Information
Version2.0
Creation Date2012-05-31 13:03:45 -0600
Update Date2015-09-13 12:56:09 -0600
Secondary Accession Numbers
  • ECMDB01044
Identification
Name:2'-Deoxyguanosine 5'-monophosphate
Description2'-Deoxyguanosine 5'-monophosphate is a derivative of the common nucleic acid GTP, or guanosine triphosphate, in which the -OH (hydroxyl) group on the 2' carbon on the nucleotide's pentose has been removed (hence the deoxy- part of the name). Additionally, the diphosphate of the name indicates that two of the phosphoryl groups of GTP have been removed, most likely by hydrolysis (Wikipedia).
Structure
Thumb
MOLSDFPDBSMILESInChI
Synonyms:
  • 2'-Deoxy-5'-GMP
  • 2'-Deoxy-5'-guanylate
  • 2'-Deoxy-5'-guanylic acid
  • 2'-Deoxy-GMP
  • 2'-Deoxy-Guanosine 5'-(dihydrogen phosphate)
  • 2'-Deoxy-guanosine 5'-(dihydrogen phosphoric acid)
  • 2'-Deoxy-Guanosine 5'-phosphate
  • 2'-Deoxy-guanosine 5'-phosphoric acid
  • 2'-Deoxy-Guanosine phosphate
  • 2'-Deoxy-guanosine phosphoric acid
  • 2'-Deoxyguanosine 5'-monophosphate
  • 2'-Deoxyguanosine 5'-monophosphoric acid
  • 2'-Deoxyguanosine 5'-phosphate
  • 2'-Deoxyguanosine 5'-phosphoric acid
  • 2'-Deoxyguanosine-5'-phosphate
  • 2'-Deoxyguanosine-5'-phosphoric acid
  • 2'-Deoxyguanylate
  • 2'-Deoxyguanylic acid
  • 2'-DG-5'-MP
  • 2'-dGMP
  • Deoxy-GMP
  • Deoxyguanosine 5'-monophosphate
  • Deoxyguanosine 5'-monophosphoric acid
  • Deoxyguanosine 5'-phosphate
  • Deoxyguanosine 5'-phosphoric acid
  • Deoxyguanosine-phosphate
  • Deoxyguanosine-phosphoric acid
  • DGMP
  • G
  • Guanine riboside
  • Vernine
Chemical Formula:C10H14N5O7P
Weight:Average: 347.2212
Monoisotopic: 347.063084339
InChI Key:LTFMZDNNPPEQNG-KVQBGUIXSA-N
InChI:InChI=1S/C10H14N5O7P/c11-10-13-8-7(9(17)14-10)12-3-15(8)6-1-4(16)5(22-6)2-21-23(18,19)20/h3-6,16H,1-2H2,(H2,18,19,20)(H3,11,13,14,17)/t4-,5+,6+/m0/s1
CAS number:902-04-5
IUPAC Name:{[(2R,3S,5R)-5-(2-amino-6-oxo-6,9-dihydro-3H-purin-9-yl)-3-hydroxyoxolan-2-yl]methoxy}phosphonic acid
Traditional IUPAC Name:deoxyguanylate
SMILES:NC1=NC(=O)C2=C(N1)N(C=N2)[C@H]1C[C@H](O)[C@@H](COP(O)(O)=O)O1
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.
KingdomOrganic compounds
Super ClassNucleosides, nucleotides, and analogues
ClassPurine nucleotides
Sub ClassPurine deoxyribonucleotides
Direct ParentPurine 2'-deoxyribonucleoside monophosphates
Alternative Parents
Substituents
  • Purine 2'-deoxyribonucleoside monophosphate
  • Imidazopyrimidine
  • Purine
  • Hydroxypyrimidine
  • Monoalkyl phosphate
  • N-substituted imidazole
  • Organic phosphoric acid derivative
  • Phosphoric acid ester
  • Alkyl phosphate
  • Pyrimidine
  • Azole
  • Imidazole
  • Heteroaromatic compound
  • Tetrahydrofuran
  • Secondary alcohol
  • Organoheterocyclic compound
  • Azacycle
  • Oxacycle
  • Organooxygen compound
  • Organonitrogen compound
  • Hydrocarbon derivative
  • Organic oxide
  • Organopnictogen compound
  • Organic oxygen compound
  • Organic nitrogen compound
  • Alcohol
  • Aromatic heteropolycyclic compound
Molecular FrameworkAromatic heteropolycyclic compounds
External Descriptors
Physical Properties
State:Solid
Charge:-1
Melting point:Not Available
Experimental Properties:
PropertyValueSource
Predicted Properties
PropertyValueSource
Water Solubility2.7 g/LALOGPS
logP-1.9ALOGPS
logP-2.8ChemAxon
logS-2.1ALOGPS
pKa (Strongest Acidic)1.21ChemAxon
pKa (Strongest Basic)2.62ChemAxon
Physiological Charge-1ChemAxon
Hydrogen Acceptor Count10ChemAxon
Hydrogen Donor Count5ChemAxon
Polar Surface Area181.52 ŲChemAxon
Rotatable Bond Count4ChemAxon
Refractivity73.55 m³·mol⁻¹ChemAxon
Polarizability29.72 ųChemAxon
Number of Rings3ChemAxon
Bioavailability1ChemAxon
Rule of FiveYesChemAxon
Ghose FilterYesChemAxon
Veber's RuleYesChemAxon
MDDR-like RuleYesChemAxon
Biological Properties
Cellular Locations:Cytoplasm
Reactions:
dGTP + Water > 2'-Deoxyguanosine 5'-monophosphate + Hydrogen ion + Pyrophosphate
2'-Deoxyguanosine 5'-monophosphate + Water > Deoxyguanosine + Phosphate
Adenosine triphosphate + 2'-Deoxyguanosine 5'-monophosphate <> ADP + dGDP
dGTP + Water <> 2'-Deoxyguanosine 5'-monophosphate + Pyrophosphate
2'-Deoxyguanosine 5'-monophosphate + Water <> Deoxyguanosine + Phosphate
Adenosine triphosphate + 2'-Deoxyguanosine 5'-monophosphate <> ADP + dGDP
dGTP + Water > Hydrogen ion + 2'-Deoxyguanosine 5'-monophosphate + Pyrophosphate
Adenosine triphosphate + 2 2'-Deoxyguanosine 5'-monophosphate <> ADP + dGDP
SMPDB Pathways:Not Available
KEGG Pathways:
EcoCyc Pathways:Not Available
Concentrations
ConcentrationStrainMediaGrowth StatusGrowth SystemTemperatureDetails
51± 0 uMK12 NCM3722Gutnick minimal complete medium (4.7 g/L KH2PO4; 13.5 g/L K2HPO4; 1 g/L K2SO4; 0.1 g/L MgSO4-7H2O; 10 mM NH4Cl) with 4 g/L glucoseMid-Log PhaseShake flask and filter culture37 oCPMID: 19561621
Find out more about how we convert literature concentrations.
Spectra
Spectra:
Spectrum TypeDescriptionSplash Key
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (Non-derivatized) - 70eV, Positivesplash10-0002-9412000000-b0aa92c3ffa6b5b0890cView in MoNA
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (1 TMS) - 70eV, Positivesplash10-03dm-9422100000-bc551a9549f9ae975b71View in MoNA
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (Non-derivatized) - 70eV, PositiveNot AvailableView in JSpectraViewer
LC-MS/MSLC-MS/MS Spectrum - Quattro_QQQ 10V, Positive (Annotated)splash10-0fr2-0598000000-21b063e2aff7146d8568View in MoNA
LC-MS/MSLC-MS/MS Spectrum - LC-ESI-QTOF (UPLC Q-Tof Premier, Waters) , Positivesplash10-0udi-0900000000-d2858e957ac8a4c91e79View in MoNA
LC-MS/MSLC-MS/MS Spectrum - LC-ESI-QTOF (UPLC Q-Tof Premier, Waters) , Negativesplash10-004j-9203000000-40bcf8d5e1ae6813c4f7View in MoNA
LC-MS/MSLC-MS/MS Spectrum - LC-ESI-QTOF , negativesplash10-004j-9203000000-40bcf8d5e1ae6813c4f7View in MoNA
LC-MS/MSLC-MS/MS Spectrum - LC-ESI-QTOF , positivesplash10-0udi-0900000000-dab30b9a6de3477fa70eView in MoNA
LC-MS/MSLC-MS/MS Spectrum - 10V, Negativesplash10-002b-6109000000-6e5f13e1030d907bf450View in MoNA
LC-MS/MSLC-MS/MS Spectrum - 20V, Negativesplash10-004i-9200000000-c3273057674f4f74157bView in MoNA
LC-MS/MSLC-MS/MS Spectrum - 10V, Negativesplash10-002b-6009000000-303a1b69aa5c35e59b53View in MoNA
LC-MS/MSLC-MS/MS Spectrum - 40V, Negativesplash10-004i-9200000000-5a760c04146b7ec031d7View in MoNA
LC-MS/MSLC-MS/MS Spectrum - 40V, Negativesplash10-004i-9300000000-d435ed7c5cdb98529682View in MoNA
LC-MS/MSLC-MS/MS Spectrum - 20V, Negativesplash10-004i-9100000000-41c0a9342f54a46fa4e4View in MoNA
LC-MS/MSLC-MS/MS Spectrum - 40V, Positivesplash10-000i-2900000000-68f72700dfdbb0374a85View in MoNA
LC-MS/MSLC-MS/MS Spectrum - 10V, Positivesplash10-000j-0905000000-26458e3261a5441d9304View in MoNA
LC-MS/MSLC-MS/MS Spectrum - 40V, Positivesplash10-0udr-1900000000-7a7e7e8e0b0145b7230dView in MoNA
LC-MS/MSLC-MS/MS Spectrum - 20V, Positivesplash10-0udi-1900000000-a0ce6815866f122bcce0View in MoNA
LC-MS/MSLC-MS/MS Spectrum - 10V, Positivesplash10-000i-0901000000-415ae3ba37bc56d4a402View in MoNA
LC-MS/MSLC-MS/MS Spectrum - 20V, Positivesplash10-000i-1900000000-bd375d50d1fb3f236468View in MoNA
LC-MS/MSLC-MS/MS Spectrum - 10V, Positivesplash10-0udi-0900000000-6585941fd6af257d9a96View in MoNA
LC-MS/MSLC-MS/MS Spectrum - 40V, Positivesplash10-000i-2900000000-303e1f2bb06730d8520dView in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Positivesplash10-0udi-0901000000-e4234086a26601ce5af3View in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Positivesplash10-0udi-0900000000-566d720734de1bad5cd6View in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Positivesplash10-0udi-0900000000-5d4689698c352d2a2f45View in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Negativesplash10-002b-6309000000-10f0b25fe6368edd1660View in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Negativesplash10-004i-9500000000-d531006102bbcb9090d1View in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Negativesplash10-004i-9100000000-a08be881b0ccce87df8aView in MoNA
1D NMR1H NMR SpectrumNot AvailableView in JSpectraViewer
1D NMR1H NMR SpectrumNot AvailableView in JSpectraViewer
1D NMR13C NMR SpectrumNot AvailableView in JSpectraViewer
1D NMR1H NMR SpectrumNot AvailableView in JSpectraViewer
1D NMR13C NMR SpectrumNot AvailableView in JSpectraViewer
1D NMR1H NMR SpectrumNot AvailableView in JSpectraViewer
1D NMR13C NMR SpectrumNot AvailableView in JSpectraViewer
1D NMR1H NMR SpectrumNot AvailableView in JSpectraViewer
1D NMR13C NMR SpectrumNot AvailableView in JSpectraViewer
1D NMR1H NMR SpectrumNot AvailableView in JSpectraViewer
1D NMR13C NMR SpectrumNot AvailableView in JSpectraViewer
1D NMR1H NMR SpectrumNot AvailableView in JSpectraViewer
1D NMR13C NMR SpectrumNot AvailableView in JSpectraViewer
1D NMR1H NMR SpectrumNot AvailableView in JSpectraViewer
1D NMR13C NMR SpectrumNot AvailableView in JSpectraViewer
1D NMR1H NMR SpectrumNot AvailableView in JSpectraViewer
1D NMR13C NMR SpectrumNot AvailableView in JSpectraViewer
1D NMR1H NMR SpectrumNot AvailableView in JSpectraViewer
1D NMR13C NMR SpectrumNot AvailableView in JSpectraViewer
1D NMR1H NMR SpectrumNot AvailableView in JSpectraViewer
1D NMR13C NMR SpectrumNot AvailableView in JSpectraViewer
1D NMR1H NMR SpectrumNot AvailableView in JSpectraViewer
2D NMR[1H,13C] 2D NMR SpectrumNot AvailableView in JSpectraViewer
References
References:
  • Bennett, B. D., Kimball, E. H., Gao, M., Osterhout, R., Van Dien, S. J., Rabinowitz, J. D. (2009). "Absolute metabolite concentrations and implied enzyme active site occupancy in Escherichia coli." Nat Chem Biol 5:593-599. Pubmed: 19561621
  • Kanehisa, M., Goto, S., Sato, Y., Furumichi, M., Tanabe, M. (2012). "KEGG for integration and interpretation of large-scale molecular data sets." Nucleic Acids Res 40:D109-D114. Pubmed: 22080510
  • Keseler, I. M., Collado-Vides, J., Santos-Zavaleta, A., Peralta-Gil, M., Gama-Castro, S., Muniz-Rascado, L., Bonavides-Martinez, C., Paley, S., Krummenacker, M., Altman, T., Kaipa, P., Spaulding, A., Pacheco, J., Latendresse, M., Fulcher, C., Sarker, M., Shearer, A. G., Mackie, A., Paulsen, I., Gunsalus, R. P., Karp, P. D. (2011). "EcoCyc: a comprehensive database of Escherichia coli biology." Nucleic Acids Res 39:D583-D590. Pubmed: 21097882
  • van der Werf, M. J., Overkamp, K. M., Muilwijk, B., Coulier, L., Hankemeier, T. (2007). "Microbial metabolomics: toward a platform with full metabolome coverage." Anal Biochem 370:17-25. Pubmed: 17765195
  • Warnecke A, Fichtner I, Garmann D, Jaehde U, Kratz F: Synthesis and biological activity of water-soluble maleimide derivatives of the anticancer drug carboplatin designed as albumin-binding prodrugs. Bioconjug Chem. 2004 Nov-Dec;15(6):1349-59. Pubmed: 15546202
Synthesis Reference:Reichard, Peter. Formation of deoxyguanosine 5'-phosphate from guanosine 5'-phosphate with enzymes from chick embryos. Biochimica et Biophysica Acta (1960), 41 368-9.
Material Safety Data Sheet (MSDS)Download (PDF)
External Links:
ResourceLink
CHEBI ID16192
HMDB IDHMDB01044
Pubchem Compound ID65059
Kegg IDC00362
ChemSpider ID58570
Wikipedia IDDeoxyguanosine_monophosphate
BioCyc IDDGMP
EcoCyc IDDGMP
Ligand ExpoPG7

Enzymes

Protein Details
1. Protein ushA
General function:
Involved in hydrolase activity
Specific function:
Degradation of external UDP-glucose to uridine monophosphate and glucose-1-phosphate, which can then be used by the cell
Gene Name:
ushA
Uniprot ID:
P07024
Molecular weight:
60824
Reactions
UDP-sugar + H(2)O = UMP + alpha-D-aldose 1-phosphate.
A 5'-ribonucleotide + H(2)O = a ribonucleoside + phosphate.
Protein Details
2. Multifunctional protein surE
General function:
Involved in hydrolase activity
Specific function:
Nucleotidase with a broad substrate specificity as it can dephosphorylate various ribo- and deoxyribonucleoside 5'- monophosphates and ribonucleoside 3'-monophosphates with highest affinity to 3'-AMP. Also hydrolyzes polyphosphate (exopolyphosphatase activity) with the preference for short-chain- length substrates (P20-25). Might be involved in the regulation of dNTP and NTP pools, and in the turnover of 3'-mononucleotides produced by numerous intracellular RNases (T1, T2, and F) during the degradation of various RNAs. Also plays a significant physiological role in stress-response and is required for the survival of E.coli in stationary growth phase
Gene Name:
surE
Uniprot ID:
P0A840
Molecular weight:
26900
Reactions
A 5'-ribonucleotide + H(2)O = a ribonucleoside + phosphate.
A 3'-ribonucleotide + H(2)O = a ribonucleoside + phosphate.
(Polyphosphate)(n) + H(2)O = (polyphosphate)(n-1) + phosphate.
Protein Details
3. 5'-nucleotidase yjjG
General function:
Involved in catalytic activity
Specific function:
Nucleotidase that shows high phosphatase activity toward three nucleoside 5'-monophosphates, UMP, dUMP, and dTMP, and very low activity against TDP, IMP, UDP, GMP, dGMP, AMP, dAMP, and 6- phosphogluconate. Is strictly specific to substrates with 5'- phosphates and shows no activity against nucleoside 2'- or 3'- monophosphates. Might be involved in the pyrimidine nucleotide substrate cycles
Gene Name:
yjjG
Uniprot ID:
P0A8Y1
Molecular weight:
25300
Reactions
A 5'-ribonucleotide + H(2)O = a ribonucleoside + phosphate.
Protein Details
4. Class B acid phosphatase
General function:
Involved in acid phosphatase activity
Specific function:
Dephosphorylates several organic phosphomonoesters and catalyzes the transfer of low-energy phosphate groups from phosphomonoesters to hydroxyl groups of various organic compounds. Preferentially acts on aryl phosphoesters. Might function as a broad-spectrum dephosphorylating enzyme able to scavenge both 3'- and 5'-nucleotides and also additional organic phosphomonoesters
Gene Name:
aphA
Uniprot ID:
P0AE22
Molecular weight:
26103
Reactions
A phosphate monoester + H(2)O = an alcohol + phosphate.
Protein Details
5. Protein mazG
General function:
Involved in nucleoside-triphosphate diphosphatase activity
Specific function:
Specific function unknown
Gene Name:
mazG
Uniprot ID:
P0AEY3
Molecular weight:
30412
Reactions
ATP + H(2)O = AMP + diphosphate.
Protein Details
6. Nucleoside-triphosphatase rdgB
General function:
Involved in hydrolase activity
Specific function:
Hydrolyzes O6 atom-containing purine bases deoxyinosine triphosphate (dITP) and xanthosine triphosphate (XTP) as well as 2'-deoxy-N-6-hydroxylaminopurine triposphate (dHAPTP) to nucleotide monophosphate and pyrophosphate. Probably excludes non- standard purines from DNA precursor pool, preventing thus incorporation into DNA and avoiding chromosomal lesions
Gene Name:
rdgB
Uniprot ID:
P52061
Molecular weight:
21039
Reactions
A nucleoside triphosphate + H(2)O = a nucleotide + diphosphate.
Protein Details
7. Guanylate kinase
General function:
Involved in protein binding
Specific function:
Essential for recycling GMP and indirectly, cGMP
Gene Name:
gmk
Uniprot ID:
P60546
Molecular weight:
23593
Reactions
ATP + GMP = ADP + GDP.
Protein Details
8. 5'-nucleotidase yfbR
General function:
Involved in catalytic activity
Specific function:
Nucleotidase that shows strict specificity toward deoxyribonucleoside 5'-monophosphates and does not dephosphorylate 5'-ribonucleotides or ribonucleoside 3'-monophosphates. Might be involved in the regulation of all dNTP pools in E.coli
Gene Name:
yfbR
Uniprot ID:
P76491
Molecular weight:
22708
Reactions
A 5'-ribonucleotide + H(2)O = a ribonucleoside + phosphate.
Protein Details
9. Mutator mutT protein
General function:
Replication, recombination and repair
Specific function:
Involved in the GO system responsible for removing an oxidatively damaged form of guanine (7,8-dihydro-8-oxoguanine) from DNA and the nucleotide pool. 8-oxo-dGTP is inserted opposite dA and dC residues of template DNA with almost equal efficiency thus leading to A.T to G.C transversions. MutT specifically degrades 8-oxo-dGTP to the monophosphate
Gene Name:
mutT
Uniprot ID:
P08337
Molecular weight:
14927
Reactions
8-oxo-dGTP + H(2)O = 8-oxo-dGMP + diphosphate.

Transporters

Protein Details
1. Outer membrane protein N
General function:
Involved in transporter activity
Specific function:
Non-specific porin
Gene Name:
ompN
Uniprot ID:
P77747
Molecular weight:
41220
Protein Details
2. Outer membrane pore protein E
General function:
Involved in transporter activity
Specific function:
Uptake of inorganic phosphate, phosphorylated compounds, and some other negatively charged solutes
Gene Name:
phoE
Uniprot ID:
P02932
Molecular weight:
38922
Protein Details
3. Outer membrane protein F
General function:
Involved in transporter activity
Specific function:
OmpF is a porin that forms passive diffusion pores which allow small molecular weight hydrophilic materials across the outer membrane. It is also a receptor for the bacteriophage T2
Gene Name:
ompF
Uniprot ID:
P02931
Molecular weight:
39333
Protein Details
4. Outer membrane protein C
General function:
Involved in transporter activity
Specific function:
Forms passive diffusion pores which allow small molecular weight hydrophilic materials across the outer membrane
Gene Name:
ompC
Uniprot ID:
P06996
Molecular weight:
40368