dGMP (YMDB00506)

Identification
YMDB IDYMDB00506
NamedGMP
SpeciesSaccharomyces cerevisiae
StrainBaker's yeast
Description2'-Deoxyguanosine 5'-monophosphate, also known as deoxyguanylic acid or 2'-deoxy-GMP, 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. 2'-Deoxyguanosine 5'-monophosphate is a moderately basic compound (based on its pKa). 2'-Deoxyguanosine 5'-monophosphate exists in all living species, ranging from bacteria to humans.
Structure
Thumb
MOLSDFPDBSMILESInChI
Synonyms
  • 2-deoxyguanosine 5-monophosphate
  • 2-deoxyguanosine 5-phosphate
  • 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'-phosphate
  • 2'-deoxy-Guanosine phosphate
  • 2'-Deoxyguanosine 5'-monophosphate
  • 2'-Deoxyguanosine 5'-monophosphic acid
  • 2'-Deoxyguanosine 5'-phosphate
  • 2'-Deoxyguanosine 5'-phosphoric acid
  • 2'-Deoxyguanosine 5'MP
  • 2'-deoxyguanosine-5'-phosphate
  • 2'-Deoxyguanylate
  • 2'-Deoxyguanylic acid
  • 2'-dG-5'-MP
  • 2'-dGMP
  • 5'-Deoxyguanylic acid
  • 5'-DGMP
  • 5'-Guanylic acid, 2'-deoxy-
  • Deoxy GMP
  • Deoxy-GMP
  • Deoxyguanosine 5'-monophosphate
  • Deoxyguanosine 5'-phosphate
  • deoxyguanosine monophosphate
  • deoxyguanosine-phosphate
  • deoxyguanylic acid
  • dGMP
  • DGP
  • guanine riboside
  • Guanosine, 2'-deoxy-, 5'-(dihydrogen phosphate)
  • Guanosine, 2'-deoxy-, 5'-phosphoric acid
  • 2'-Deoxyguanosine 5'-(dihydrogen phosphate)
  • 2'-Deoxyguanosine 5'-(dihydrogen phosphoric acid)
  • Deoxyguanosine 5'-monophosphoric acid
  • Deoxyguanosine 5'-phosphoric acid
  • Deoxyguanosine monophosphoric acid
  • Deoxyguanylate
  • 2'-Deoxyguanosine 5'-monophosphoric acid
  • 2'-Deoxyguanosine 5'-phosphate, ion (1+)
  • 2'-Deoxyguanosine 5'-phosphate, disodium salt
CAS number902-04-5
WeightAverage: 347.2212
Monoisotopic: 347.063084339
InChI KeyLTFMZDNNPPEQNG-KVQBGUIXSA-N
InChIInChI=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
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 Namedeoxyguanylate
Chemical FormulaC10H14N5O7P
SMILESNC1=NC2=C(N=CN2[C@H]2C[C@H](O)[C@@H](COP(O)(O)=O)O2)C(=O)N1
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
StateSolid
Charge0
Melting pointNot Available
Experimental Properties
PropertyValueReference
Water SolubilityNot AvailablePhysProp
LogPNot AvailablePhysProp
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
  • mitochondrion
  • cytoplasm
Organoleptic PropertiesNot Available
SMPDB PathwaysNot Available
KEGG Pathways
Purine metabolismec00230 Map00230
SMPDB ReactionsNot Available
KEGG Reactions
water + dGMP → 2'-Deoxyguanosine + phosphate
Adenosine triphosphate + dGMP ↔ ADP + dGDP
water + dGDP → phosphate + hydron + dGMP
Concentrations
Intracellular ConcentrationsNot Available
Extracellular ConcentrationsNot Available
Spectra
Spectra
Spectrum TypeDescriptionSplash KeyView
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (Non-derivatized) - 70eV, Positivesplash10-0002-9412000000-b0aa92c3ffa6b5b0890cJSpectraViewer
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (1 TMS) - 70eV, Positivesplash10-03dm-9422100000-bc551a9549f9ae975b71JSpectraViewer
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (Non-derivatized) - 70eV, PositiveNot AvailableJSpectraViewer
LC-MS/MSLC-MS/MS Spectrum - Quattro_QQQ 10V, Positive (Annotated)splash10-0fr2-0598000000-21b063e2aff7146d8568JSpectraViewer | MoNA
LC-MS/MSLC-MS/MS Spectrum - LC-ESI-QTOF (UPLC Q-Tof Premier, Waters) , Positivesplash10-0udi-0900000000-d2858e957ac8a4c91e79JSpectraViewer | MoNA
LC-MS/MSLC-MS/MS Spectrum - LC-ESI-QTOF (UPLC Q-Tof Premier, Waters) , Negativesplash10-004j-9203000000-40bcf8d5e1ae6813c4f7JSpectraViewer | MoNA
LC-MS/MSLC-MS/MS Spectrum - LC-ESI-QTOF , negativesplash10-004j-9203000000-40bcf8d5e1ae6813c4f7JSpectraViewer | MoNA
LC-MS/MSLC-MS/MS Spectrum - LC-ESI-QTOF , positivesplash10-0udi-0900000000-dab30b9a6de3477fa70eJSpectraViewer | MoNA
LC-MS/MSLC-MS/MS Spectrum - 10V, Negativesplash10-002b-6109000000-6e5f13e1030d907bf450JSpectraViewer | MoNA
LC-MS/MSLC-MS/MS Spectrum - 20V, Negativesplash10-004i-9200000000-c3273057674f4f74157bJSpectraViewer | MoNA
LC-MS/MSLC-MS/MS Spectrum - 10V, Negativesplash10-002b-6009000000-303a1b69aa5c35e59b53JSpectraViewer | MoNA
LC-MS/MSLC-MS/MS Spectrum - 40V, Negativesplash10-004i-9200000000-5a760c04146b7ec031d7JSpectraViewer | MoNA
LC-MS/MSLC-MS/MS Spectrum - 40V, Negativesplash10-004i-9300000000-d435ed7c5cdb98529682JSpectraViewer | MoNA
LC-MS/MSLC-MS/MS Spectrum - 20V, Negativesplash10-004i-9100000000-41c0a9342f54a46fa4e4JSpectraViewer | MoNA
LC-MS/MSLC-MS/MS Spectrum - 40V, Positivesplash10-000i-2900000000-68f72700dfdbb0374a85JSpectraViewer | MoNA
LC-MS/MSLC-MS/MS Spectrum - 10V, Positivesplash10-000j-0905000000-26458e3261a5441d9304JSpectraViewer | MoNA
LC-MS/MSLC-MS/MS Spectrum - 40V, Positivesplash10-0udr-1900000000-7a7e7e8e0b0145b7230dJSpectraViewer | MoNA
LC-MS/MSLC-MS/MS Spectrum - 20V, Positivesplash10-0udi-1900000000-a0ce6815866f122bcce0JSpectraViewer | MoNA
LC-MS/MSLC-MS/MS Spectrum - 10V, Positivesplash10-000i-0901000000-415ae3ba37bc56d4a402JSpectraViewer | MoNA
LC-MS/MSLC-MS/MS Spectrum - 20V, Positivesplash10-000i-1900000000-bd375d50d1fb3f236468JSpectraViewer | MoNA
LC-MS/MSLC-MS/MS Spectrum - 10V, Positivesplash10-0udi-0900000000-6585941fd6af257d9a96JSpectraViewer | MoNA
LC-MS/MSLC-MS/MS Spectrum - 40V, Positivesplash10-000i-2900000000-303e1f2bb06730d8520dJSpectraViewer | MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Positivesplash10-0udi-0901000000-e4234086a26601ce5af3JSpectraViewer
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Positivesplash10-0udi-0900000000-566d720734de1bad5cd6JSpectraViewer
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Positivesplash10-0udi-0900000000-5d4689698c352d2a2f45JSpectraViewer
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Negativesplash10-002b-6309000000-10f0b25fe6368edd1660JSpectraViewer
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Negativesplash10-004i-9500000000-d531006102bbcb9090d1JSpectraViewer
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Negativesplash10-004i-9100000000-a08be881b0ccce87df8aJSpectraViewer
1D NMR1H NMR SpectrumNot AvailableJSpectraViewer
1D NMR1H NMR SpectrumNot AvailableJSpectraViewer
1D NMR13C NMR SpectrumNot AvailableJSpectraViewer
1D NMR1H NMR SpectrumNot AvailableJSpectraViewer
1D NMR13C NMR SpectrumNot AvailableJSpectraViewer
1D NMR1H NMR SpectrumNot AvailableJSpectraViewer
1D NMR13C NMR SpectrumNot AvailableJSpectraViewer
1D NMR1H NMR SpectrumNot AvailableJSpectraViewer
1D NMR13C NMR SpectrumNot AvailableJSpectraViewer
1D NMR1H NMR SpectrumNot AvailableJSpectraViewer
1D NMR13C NMR SpectrumNot AvailableJSpectraViewer
1D NMR1H NMR SpectrumNot AvailableJSpectraViewer
1D NMR13C NMR SpectrumNot AvailableJSpectraViewer
1D NMR1H NMR SpectrumNot AvailableJSpectraViewer
1D NMR13C NMR SpectrumNot AvailableJSpectraViewer
1D NMR1H NMR SpectrumNot AvailableJSpectraViewer
1D NMR13C NMR SpectrumNot AvailableJSpectraViewer
1D NMR1H NMR SpectrumNot AvailableJSpectraViewer
1D NMR13C NMR SpectrumNot AvailableJSpectraViewer
1D NMR1H NMR SpectrumNot AvailableJSpectraViewer
1D NMR13C NMR SpectrumNot AvailableJSpectraViewer
1D NMR1H NMR SpectrumNot AvailableJSpectraViewer
2D NMR[1H,13C] 2D NMR SpectrumNot AvailableJSpectraViewer
References
References:
  • Herrgard, M. J., Swainston, N., Dobson, P., Dunn, W. B., Arga, K. Y., Arvas, M., Bluthgen, N., Borger, S., Costenoble, R., Heinemann, M., Hucka, M., Le Novere, N., Li, P., Liebermeister, W., Mo, M. L., Oliveira, A. P., Petranovic, D., Pettifer, S., Simeonidis, E., Smallbone, K., Spasic, I., Weichart, D., Brent, R., Broomhead, D. S., Westerhoff, H. V., Kirdar, B., Penttila, M., Klipp, E., Palsson, B. O., Sauer, U., Oliver, S. G., Mendes, P., Nielsen, J., Kell, D. B. (2008). "A consensus yeast metabolic network reconstruction obtained from a community approach to systems biology." Nat Biotechnol 26:1155-1160.18846089
  • Nookaew, I., Jewett, M. C., Meechai, A., Thammarongtham, C., Laoteng, K., Cheevadhanarak, S., Nielsen, J., Bhumiratana, S. (2008). "The genome-scale metabolic model iIN800 of Saccharomyces cerevisiae and its validation: a scaffold to query lipid metabolism." BMC Syst Biol 2:71.18687109
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.
External Links:
ResourceLink
CHEBI ID16192
HMDB IDHMDB01044
Pubchem Compound ID65059
Kegg IDC00362
ChemSpider ID24604718
FOODB IDFDB022388
WikipediaDeoxyguanosine_monophosphate
BioCyc IDDGMP

Enzymes

Protein Details
1. Guanylate kinase
General function:
Involved in protein binding
Specific function:
Essential for recycling GMP and indirectly, cGMP
Gene Name:
GUK1
Uniprot ID:
P15454
Molecular weight:
20637.19922
Reactions
ATP + GMP → ADP + GDP.

Transporters

Protein Details
1. Uncharacterized mitochondrial carrier YIL006W
General function:
Involved in binding
Specific function:
Not Available
Gene Name:
Not Available
Uniprot ID:
P40556
Molecular weight:
41954.0