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Xanthylic acid (YMDB00289)

Identification
YMDB IDYMDB00289
NameXanthylic acid
SpeciesSaccharomyces cerevisiae
StrainBaker's yeast
DescriptionXanthylic acid, also known as XMP or xanthylate, belongs to the class of organic compounds known as purine ribonucleoside monophosphates. These are nucleotides consisting of a purine base linked to a ribose to which one monophosphate group is attached. Xanthylic acid is an extremely weak basic (essentially neutral) compound (based on its pKa). Xanthylic acid exists in all living species, ranging from bacteria to humans.
Structure
Thumb
MOLSDFPDBSMILESInChI
Synonyms
  • (9-D-ribosylxanthine)-5'-phosphate
  • 5'-xanthonylate monophosphate
  • Xanthosine 5'-phosphate
  • Xanthosine 5'-phosphic acid
  • xanthosine-5'-P
  • xanthosine-5'-phosphate
  • XMP
  • Xanthosine monophosphate
  • (9-D-Ribosylxanthine)-5'-phosphoric acid
  • Xanthylate
  • Xanthosine 5'-phosphoric acid
  • Xanthosine monophosphoric acid
  • Xanthosine monophosphate, 8-(14)C-labeled
  • Xanthosine 5'-monophosphate
  • Xanthosine 5’-monophosphate
  • Xanthosine 5’-phosphate
  • Xanthylic acid
CAS number523-98-8
WeightAverage: 364.2054
Monoisotopic: 364.042014546
InChI KeyDCTLYFZHFGENCW-UUOKFMHZSA-N
InChIInChI=1S/C10H13N4O9P/c15-5-3(1-22-24(19,20)21)23-9(6(5)16)14-2-11-4-7(14)12-10(18)13-8(4)17/h2-3,5-6,9,15-16H,1H2,(H2,19,20,21)(H2,12,13,17,18)/t3-,5-,6-,9-/m1/s1
IUPAC Name{[(2R,3S,4R,5R)-5-(2,6-dioxo-2,3,6,9-tetrahydro-1H-purin-9-yl)-3,4-dihydroxyoxolan-2-yl]methoxy}phosphonic acid
Traditional IUPAC Namexanthosine monophosphate
Chemical FormulaC10H13N4O9P
SMILES[H]O[C@@]1([H])[C@@]([H])(O[C@]([H])(C([H])([H])OP(=O)(O[H])O[H])[C@@]1([H])O[H])N1C([H])=NC2=C1N([H])C(=O)N([H])C2=O
Chemical Taxonomy
Description belongs to the class of organic compounds known as purine ribonucleoside monophosphates. These are nucleotides consisting of a purine base linked to a ribose to which one monophosphate group is attached.
KingdomOrganic compounds
Super ClassNucleosides, nucleotides, and analogues
ClassPurine nucleotides
Sub ClassPurine ribonucleotides
Direct ParentPurine ribonucleoside monophosphates
Alternative Parents
Substituents
  • Purine ribonucleoside monophosphate
  • Pentose phosphate
  • Pentose-5-phosphate
  • Glycosyl compound
  • N-glycosyl compound
  • Xanthine
  • 6-oxopurine
  • Monosaccharide phosphate
  • Pentose monosaccharide
  • Purinone
  • Imidazopyrimidine
  • Purine
  • Alkaloid or derivatives
  • Monoalkyl phosphate
  • Pyrimidone
  • Monosaccharide
  • N-substituted imidazole
  • Organic phosphoric acid derivative
  • Alkyl phosphate
  • Phosphoric acid ester
  • Pyrimidine
  • Heteroaromatic compound
  • Azole
  • Vinylogous amide
  • Imidazole
  • Tetrahydrofuran
  • Lactam
  • 1,2-diol
  • Urea
  • Secondary alcohol
  • Azacycle
  • Oxacycle
  • Organoheterocyclic compound
  • Alcohol
  • Organic oxide
  • Organonitrogen compound
  • Organopnictogen compound
  • Organic oxygen compound
  • Organooxygen compound
  • Hydrocarbon derivative
  • Organic nitrogen compound
  • 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 Solubility2.49 g/LALOGPS
logP-2ALOGPS
logP-2.2ChemAxon
logS-2.2ALOGPS
pKa (Strongest Acidic)1.26ChemAxon
pKa (Strongest Basic)0.069ChemAxon
Physiological Charge-2ChemAxon
Hydrogen Acceptor Count9ChemAxon
Hydrogen Donor Count6ChemAxon
Polar Surface Area192.47 ŲChemAxon
Rotatable Bond Count4ChemAxon
Refractivity73.08 m³·mol⁻¹ChemAxon
Polarizability29.99 ųChemAxon
Number of Rings3ChemAxon
Bioavailability1ChemAxon
Rule of FiveYesChemAxon
Ghose FilterYesChemAxon
Veber's RuleYesChemAxon
MDDR-like RuleYesChemAxon
Biological Properties
Cellular Locations
  • cytoplasm
Organoleptic PropertiesNot Available
SMPDB Pathways
purine nucleotides de novo biosynthesisPW002478 ThumbThumb?image type=greyscaleThumb?image type=simple
KEGG Pathways
Purine metabolismec00230 Map00230
SMPDB Reactions
Inosinic acid + NAD + water → NADH + hydron + Xanthylic acid
Xanthylic acid + Adenosine triphosphate + L-Glutamine + water → Adenosine monophosphate + Pyrophosphate + L-Glutamic acid + hydron + Guanosine monophosphate
KEGG Reactions
Xanthylic acid + water → phosphate + xanthosine
Adenosine triphosphate + Xanthylic acid + water + L-Glutamine → Adenosine monophosphate + Pyrophosphate + Guanosine monophosphate + L-Glutamic acid + hydron
Inosinic acid + NAD + water → NADH + Xanthylic acid + hydron
Xanthine + Phosphoribosyl pyrophosphate → Pyrophosphate + Xanthylic acid
Concentrations
Intracellular ConcentrationsNot Available
Extracellular ConcentrationsNot Available
Spectra
Spectra
Spectrum TypeDescriptionSplash KeyView
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (Non-derivatized) - 70eV, Positivesplash10-0002-9613000000-3054f73e4c9456039ed6JSpectraViewer
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (2 TMS) - 70eV, Positivesplash10-01ot-9521200000-1e6fc3c628d8ebd23b37JSpectraViewer
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (Non-derivatized) - 70eV, PositiveNot AvailableJSpectraViewer
LC-MS/MSLC-MS/MS Spectrum - LC-ESI-QTOF , negativesplash10-0ik9-7964000000-bce7ee60221f82790f35JSpectraViewer | MoNA
LC-MS/MSLC-MS/MS Spectrum - LC-ESI-QTOF , positivesplash10-0002-9400000000-05c1ae772c001a15a8c6JSpectraViewer | MoNA
LC-MS/MSLC-MS/MS Spectrum - 35V, Positivesplash10-0002-9200000000-743d2f19ea30c814c56aJSpectraViewer | MoNA
LC-MS/MSLC-MS/MS Spectrum - 10V, Positivesplash10-0002-9210000000-f36c079a2869c6c7c63dJSpectraViewer | MoNA
LC-MS/MSLC-MS/MS Spectrum - 20V, Positivesplash10-0002-9300000000-0cea344051256ed9d642JSpectraViewer | MoNA
LC-MS/MSLC-MS/MS Spectrum - 40V, Positivesplash10-0002-9300000000-1295bb6a6dfffef31dd2JSpectraViewer | MoNA
LC-MS/MSLC-MS/MS Spectrum - 20V, Positivesplash10-0002-9400000000-7125a3a52d3308d6b367JSpectraViewer | MoNA
LC-MS/MSLC-MS/MS Spectrum - 40V, Negativesplash10-0fb9-9400000000-f93509061523b8f0b012JSpectraViewer | MoNA
LC-MS/MSLC-MS/MS Spectrum - 10V, Positivesplash10-0002-9310000000-a910c200bfc66c8e1c46JSpectraViewer | MoNA
LC-MS/MSLC-MS/MS Spectrum - 40V, Positivesplash10-0002-9000000000-1ff54bb8d71e1ea585f2JSpectraViewer | MoNA
LC-MS/MSLC-MS/MS Spectrum - 20V, Negativesplash10-03fs-9380000000-2a0fbd1929733b4918d1JSpectraViewer | MoNA
LC-MS/MSLC-MS/MS Spectrum - 10V, Negativesplash10-03di-1039000000-f0bd4ff644ac79937301JSpectraViewer | MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Positivesplash10-0udi-0913000000-d17f1d77b992fc6e9f04JSpectraViewer
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Positivesplash10-0udi-0900000000-efbdb918f50ba610575dJSpectraViewer
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Positivesplash10-0udi-2900000000-cf070bd16aacd3dcb6fbJSpectraViewer
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Negativesplash10-0imi-6509000000-d931cb1dcaeba678220cJSpectraViewer
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Negativesplash10-0fbc-9300000000-e596281ec38113a9653cJSpectraViewer
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Negativesplash10-004i-9100000000-1caa46ecd17db343ddd3JSpectraViewer
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Positivesplash10-0udi-0900000000-ac450658003af6c0a109JSpectraViewer
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Positivesplash10-0udi-0900000000-448bfe6677d2f8fe1f3cJSpectraViewer
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Positivesplash10-0udi-1900000000-10c12403e596a9b5bf0aJSpectraViewer
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Negativesplash10-03di-3009000000-8a668987618bcd1531e7JSpectraViewer
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Negativesplash10-004i-9000000000-4b2bf772bc8415c9f24cJSpectraViewer
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Negativesplash10-004i-9201000000-907dd40cbb70b7a5c62dJSpectraViewer
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
References
References:
  • UniProt Consortium (2011). "Ongoing and future developments at the Universal Protein Resource." Nucleic Acids Res 39:D214-D219.21051339
  • Scheer, M., Grote, A., Chang, A., Schomburg, I., Munaretto, C., Rother, M., Sohngen, C., Stelzer, M., Thiele, J., Schomburg, D. (2011). "BRENDA, the enzyme information system in 2011." Nucleic Acids Res 39:D670-D676.21062828
  • 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
  • Hyle, J. W., Shaw, R. J., Reines, D. (2003). "Functional distinctions between IMP dehydrogenase genes in providing mycophenolate resistance and guanine prototrophy to yeast." J Biol Chem 278:28470-28478.12746440
Synthesis Reference:Hattori, Kyoji; Kawahara, Shin; Hagiwara, Takeshige. 5'-Xanthylic acid. Jpn. Kokai Tokkyo Koho (1985), 3 pp.
External Links:
ResourceLink
CHEBI ID15652
HMDB IDHMDB01554
Pubchem Compound ID1190
Kegg IDC00655
ChemSpider ID66054
FOODB IDFDB031254
WikipediaXanthosine_monophosphate
BioCyc IDXANTHOSINE-5-PHOSPHATE

Enzymes

Protein Details
1. GMP synthase [glutamine-hydrolyzing]
General function:
Involved in catalytic activity
Specific function:
ATP + xanthosine 5'-phosphate + L-glutamine + H(2)O = AMP + diphosphate + GMP + L-glutamate
Gene Name:
GUA1
Uniprot ID:
P38625
Molecular weight:
58481.80078
Reactions
ATP + xanthosine 5'-phosphate + L-glutamine + H(2)O → AMP + diphosphate + GMP + L-glutamate.
Protein Details
2. Probable inosine-5'-monophosphate dehydrogenase IMD4
General function:
Involved in catalytic activity
Specific function:
Inosine 5'-phosphate + NAD(+) + H(2)O = xanthosine 5'-phosphate + NADH
Gene Name:
IMD4
Uniprot ID:
P50094
Molecular weight:
56393.5
Reactions
Inosine 5'-phosphate + NAD(+) + H(2)O → xanthosine 5'-phosphate + NADH.
Protein Details
3. Probable inosine-5'-monophosphate dehydrogenase IMD3
General function:
Involved in catalytic activity
Specific function:
Inosine 5'-phosphate + NAD(+) + H(2)O = xanthosine 5'-phosphate + NADH
Gene Name:
IMD3
Uniprot ID:
P50095
Molecular weight:
56584.39844
Reactions
Inosine 5'-phosphate + NAD(+) + H(2)O → xanthosine 5'-phosphate + NADH.
Protein Details
4. Inosine-5'-monophosphate dehydrogenase IMD2
General function:
Involved in catalytic activity
Specific function:
Inosine 5'-phosphate + NAD(+) + H(2)O = xanthosine 5'-phosphate + NADH
Gene Name:
IMD2
Uniprot ID:
P38697
Molecular weight:
56529.5
Reactions
Inosine 5'-phosphate + NAD(+) + H(2)O → xanthosine 5'-phosphate + NADH.
Protein Details
5. Putative inosine-5'-monophosphate dehydrogenase IMD1
General function:
Involved in catalytic activity
Specific function:
Inosine 5'-phosphate + NAD(+) + H(2)O = xanthosine 5'-phosphate + NADH
Gene Name:
IMD1
Uniprot ID:
P39567
Molecular weight:
44385.80078
Reactions
Inosine 5'-phosphate + NAD(+) + H(2)O → xanthosine 5'-phosphate + NADH.
Protein Details
6. Xanthine phosphoribosyltransferase 1
General function:
Involved in nucleoside metabolic process
Specific function:
May act as a xanthine phosphoribosyltransferase involved in the synthesis of purine nucleotides. Such activity is however unclear in vivo
Gene Name:
XPT1
Uniprot ID:
P47165
Molecular weight:
23671.0
Reactions