Showing metabocard for Xanthylic acid (BMDB0001554)

IdentificationTaxonomyPhysical propertiesPathwaysSpectraConcentrationsLinksReferencesenzymes (5) Show 5 proteinsXML
Record Information
Version1.0
Creation Date2016-09-30 22:47:37 UTC
Update Date2020-05-21 16:28:26 UTC
BMDB IDBMDB0001554
Secondary Accession Numbers
  • BMDB01554
Metabolite Identification
Common NameXanthylic acid
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
ValueSource
(9-D-Ribosylxanthine)-5'-phosphateChEBI
Xanthosine 5'-phosphateChEBI
Xanthosine monophosphateChEBI
XMPChEBI
(9-D-Ribosylxanthine)-5'-phosphoric acidGenerator
XanthylateGenerator
Xanthosine 5'-phosphoric acidGenerator
Xanthosine monophosphoric acidGenerator
5'-Xanthonylate monophosphateHMDB
Xanthosine-5'-PHMDB
Xanthosine-5'-phosphateHMDB
Xanthosine monophosphate, 8-(14)C-labeledMeSH, HMDB
Xanthosine 5'-monophosphateHMDB
Xanthosine 5’-monophosphateHMDB
Xanthosine 5’-phosphateHMDB
Xanthylic acidHMDB
Chemical FormulaC10H13N4O9P
Average Molecular Weight364.2054
Monoisotopic Molecular Weight364.042014546
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 Namexanthosine monophosphate
CAS Registry Number523-98-8
SMILES
O[C@@H]1[C@@H](COP(O)(O)=O)O[C@H]([C@@H]1O)N1C=NC2=C1NC(=O)NC2=O
InChI Identifier
InChI=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
InChI KeyDCTLYFZHFGENCW-UUOKFMHZSA-N
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
Ontology
StatusExpected but not Quantified
Origin
  • Endogenous
BiofunctionNot Available
ApplicationNot Available
Cellular locations
  • Cytoplasm
Physical Properties
StateSolid
Experimental Properties
PropertyValueReference
Melting PointNot AvailableNot Available
Boiling PointNot AvailableNot Available
Water SolubilityNot AvailableNot Available
LogPNot AvailableNot Available
Predicted Properties
PropertyValueSource
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
BioavailabilityYesChemAxon
Rule of FiveYesChemAxon
Ghose FilterYesChemAxon
Veber's RuleYesChemAxon
MDDR-like RuleYesChemAxon
Spectra
Spectra
Spectrum TypeDescriptionSplash Key
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (Non-derivatized) - 70eV, Positivesplash10-0002-9613000000-3054f73e4c9456039ed6View in MoNA
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (2 TMS) - 70eV, Positivesplash10-01ot-9521200000-1e6fc3c628d8ebd23b37View in MoNA
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (Non-derivatized) - 70eV, PositiveNot AvailableView in JSpectraViewer
LC-MS/MSLC-MS/MS Spectrum - LC-ESI-QTOF , negativesplash10-0ik9-7964000000-bce7ee60221f82790f35View in MoNA
LC-MS/MSLC-MS/MS Spectrum - LC-ESI-QTOF , positivesplash10-0002-9400000000-05c1ae772c001a15a8c6View in MoNA
LC-MS/MSLC-MS/MS Spectrum - 35V, Positivesplash10-0002-9200000000-743d2f19ea30c814c56aView in MoNA
LC-MS/MSLC-MS/MS Spectrum - 10V, Positivesplash10-0002-9210000000-f36c079a2869c6c7c63dView in MoNA
LC-MS/MSLC-MS/MS Spectrum - 20V, Positivesplash10-0002-9300000000-0cea344051256ed9d642View in MoNA
LC-MS/MSLC-MS/MS Spectrum - 40V, Positivesplash10-0002-9300000000-1295bb6a6dfffef31dd2View in MoNA
LC-MS/MSLC-MS/MS Spectrum - 20V, Positivesplash10-0002-9400000000-7125a3a52d3308d6b367View in MoNA
LC-MS/MSLC-MS/MS Spectrum - 40V, Negativesplash10-0fb9-9400000000-f93509061523b8f0b012View in MoNA
LC-MS/MSLC-MS/MS Spectrum - 10V, Positivesplash10-0002-9310000000-a910c200bfc66c8e1c46View in MoNA
LC-MS/MSLC-MS/MS Spectrum - 40V, Positivesplash10-0002-9000000000-1ff54bb8d71e1ea585f2View in MoNA
LC-MS/MSLC-MS/MS Spectrum - 20V, Negativesplash10-03fs-9380000000-2a0fbd1929733b4918d1View in MoNA
LC-MS/MSLC-MS/MS Spectrum - 10V, Negativesplash10-03di-1039000000-f0bd4ff644ac79937301View in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Positivesplash10-0udi-0913000000-d17f1d77b992fc6e9f04View in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Positivesplash10-0udi-0900000000-efbdb918f50ba610575dView in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Positivesplash10-0udi-2900000000-cf070bd16aacd3dcb6fbView in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Negativesplash10-0imi-6509000000-d931cb1dcaeba678220cView in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Negativesplash10-0fbc-9300000000-e596281ec38113a9653cView in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Negativesplash10-004i-9100000000-1caa46ecd17db343ddd3View in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Positivesplash10-0udi-0900000000-ac450658003af6c0a109View in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Positivesplash10-0udi-0900000000-448bfe6677d2f8fe1f3cView in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Positivesplash10-0udi-1900000000-10c12403e596a9b5bf0aView in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Negativesplash10-03di-3009000000-8a668987618bcd1531e7View in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Negativesplash10-004i-9000000000-4b2bf772bc8415c9f24cView in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Negativesplash10-004i-9201000000-907dd40cbb70b7a5c62dView in MoNA
1D NMR13C NMR Spectrum (1D, 100 MHz, D2O, predicted)Not AvailableView in JSpectraViewer
1D NMR1H NMR Spectrum (1D, 100 MHz, D2O, predicted)Not AvailableView in JSpectraViewer
1D NMR13C NMR Spectrum (1D, 1000 MHz, D2O, predicted)Not AvailableView in JSpectraViewer
1D NMR1H NMR Spectrum (1D, 1000 MHz, D2O, predicted)Not AvailableView in JSpectraViewer
1D NMR13C NMR Spectrum (1D, 200 MHz, D2O, predicted)Not AvailableView in JSpectraViewer
1D NMR1H NMR Spectrum (1D, 200 MHz, D2O, predicted)Not AvailableView in JSpectraViewer
1D NMR13C NMR Spectrum (1D, 300 MHz, D2O, predicted)Not AvailableView in JSpectraViewer
1D NMR1H NMR Spectrum (1D, 300 MHz, D2O, predicted)Not AvailableView in JSpectraViewer
1D NMR13C NMR Spectrum (1D, 400 MHz, D2O, predicted)Not AvailableView in JSpectraViewer
1D NMR1H NMR Spectrum (1D, 400 MHz, D2O, predicted)Not AvailableView in JSpectraViewer
1D NMR13C NMR Spectrum (1D, 500 MHz, D2O, predicted)Not AvailableView in JSpectraViewer
1D NMR1H NMR Spectrum (1D, 500 MHz, D2O, predicted)Not AvailableView in JSpectraViewer
1D NMR13C NMR Spectrum (1D, 600 MHz, D2O, predicted)Not AvailableView in JSpectraViewer
1D NMR1H NMR Spectrum (1D, 600 MHz, D2O, predicted)Not AvailableView in JSpectraViewer
1D NMR13C NMR Spectrum (1D, 700 MHz, D2O, predicted)Not AvailableView in JSpectraViewer
1D NMR1H NMR Spectrum (1D, 700 MHz, D2O, predicted)Not AvailableView in JSpectraViewer
1D NMR13C NMR Spectrum (1D, 800 MHz, D2O, predicted)Not AvailableView in JSpectraViewer
1D NMR1H NMR Spectrum (1D, 800 MHz, D2O, predicted)Not AvailableView in JSpectraViewer
1D NMR13C NMR Spectrum (1D, 900 MHz, D2O, predicted)Not AvailableView in JSpectraViewer
1D NMR1H NMR Spectrum (1D, 900 MHz, D2O, predicted)Not AvailableView in JSpectraViewer
Biological Properties
Cellular Locations
  • Cytoplasm
Biospecimen LocationsNot Available
Pathways
Normal Concentrations
Not Available
Abnormal Concentrations
Not Available
HMDB IDHMDB0001554
DrugBank IDNot Available
Phenol Explorer Compound IDNot Available
FooDB IDFDB031254
KNApSAcK IDC00007396
Chemspider ID66054
KEGG Compound IDC00655
BioCyc IDXANTHOSINE-5-PHOSPHATE
BiGG ID35623
Wikipedia LinkXanthosine monophosphate
METLIN IDNot Available
PubChem Compound73323
PDB IDNot Available
ChEBI ID15652
References
Synthesis ReferenceHattori, Kyoji; Kawahara, Shin; Hagiwara, Takeshige. 5'-Xanthylic acid. Jpn. Kokai Tokkyo Koho (1985), 3 pp.
Material Safety Data Sheet (MSDS)Not Available
General ReferencesNot Available

Enzymes

Enzyme Details
1. Cytosolic purine 5'-nucleotidase
General function:
Involved in 5'-nucleotidase activity
Specific function:
May have a critical role in the maintenance of a constant composition of intracellular purine/pyrimidine nucleotides in cooperation with other nucleotidases. Preferentially hydrolyzes inosine 5'-monophosphate (IMP) and other purine nucleotides.
Gene Name:
NT5C2
Uniprot ID:
O46411
Molecular weight:
64841.0
Reactions
Xanthylic acid + Water → Xanthosine + Hydrogen phosphatedetails
Enzyme Details
2. Hypoxanthine-guanine phosphoribosyltransferase
General function:
Nucleotide transport and metabolism
Specific function:
Converts guanine to guanosine monophosphate, and hypoxanthine to inosine monophosphate. Transfers the 5-phosphoribosyl group from 5-phosphoribosylpyrophosphate onto the purine. Plays a central role in the generation of purine nucleotides through the purine salvage pathway (By similarity).
Gene Name:
HPRT1
Uniprot ID:
Q3SZ18
Molecular weight:
24498.0
Reactions
Xanthylic acid + Pyrophosphate → Xanthine + Phosphoribosyl pyrophosphatedetails
Enzyme Details
3. Inosine-5'-monophosphate dehydrogenase 2
General function:
Nucleotide transport and metabolism
Specific function:
Catalyzes the conversion of inosine 5'-phosphate (IMP) to xanthosine 5'-phosphate (XMP), the first committed and rate-limiting step in the de novo synthesis of guanine nucleotides, and therefore plays an important role in the regulation of cell growth. Could also have a single-stranded nucleic acid-binding activity and could play a role in RNA and/or DNA metabolism. It may also have a role in the development of malignancy and the growth progression of some tumors.
Gene Name:
IMPDH2
Uniprot ID:
Q3SWY3
Molecular weight:
55763.0
Enzyme Details
4. Inosine-5'-monophosphate dehydrogenase 1
General function:
Nucleotide transport and metabolism
Specific function:
Catalyzes the conversion of inosine 5'-phosphate (IMP) to xanthosine 5'-phosphate (XMP), the first committed and rate-limiting step in the de novo synthesis of guanine nucleotides, and therefore plays an important role in the regulation of cell growth. Could also have a single-stranded nucleic acid-binding activity and could play a role in RNA and/or DNA metabolism. It may also have a role in the development of malignancy and the growth progression of some tumors.
Gene Name:
IMPDH1
Uniprot ID:
A0JNA3
Molecular weight:
55424.0
Reactions
Inosinic acid + NAD + Water → Xanthylic acid + NADHdetails
Enzyme Details
5. GMPS protein
General function:
Not Available
Specific function:
Not Available
Gene Name:
GMPS
Uniprot ID:
Q2T9U0
Molecular weight:
77865.0
Reactions
Adenosine triphosphate + Xanthylic acid + Water + L-Glutamine → Adenosine monophosphate + Pyrophosphate + L-Glutamic acid + Guanosine monophosphatedetails
Adenosine triphosphate + Xanthylic acid + Ammonia → Adenosine monophosphate + Pyrophosphate + Guanosine monophosphatedetails