Showing metabocard for IDP (BMDB0003335)

IdentificationTaxonomyPhysical propertiesPathwaysSpectraConcentrationsLinksReferencesenzymes (2) Show 2 proteinsXML
Record Information
Version1.0
Creation Date2016-09-30 23:03:46 UTC
Update Date2020-05-21 16:27:08 UTC
BMDB IDBMDB0003335
Secondary Accession Numbers
  • BMDB03335
Metabolite Identification
Common NameIDP
DescriptionIDP, also known as riboxin or 5'-IDP, belongs to the class of organic compounds known as purine ribonucleoside diphosphates. These are purine ribobucleotides with diphosphate group linked to the ribose moiety. IDP is a moderately basic compound (based on its pKa). IDP exists in all living species, ranging from bacteria to humans.
Structure
Thumb
MOLSDFPDBSMILESInChI
Synonyms
ValueSource
5'-IDPHMDB
Inosine 5'-(trihydrogen diphosphate)HMDB
Inosine 5'-(trihydrogen pyrophosphate)HMDB
Inosine 5'-diphosphateHMDB
Inosine 5'-pyrophosphateHMDB
Inosine diphosphateHMDB
Inosine pyrophosphateHMDB
RiboxinHMDB
RiboxineHMDB
Diphosphate, inosineHMDB
Pyrophosphate, inosineHMDB
Chemical FormulaC10H14N4O11P2
Average Molecular Weight428.1859
Monoisotopic Molecular Weight428.013430334
IUPAC Name[({[(2R,3S,4R)-3,4-dihydroxy-5-(6-oxo-6,9-dihydro-3H-purin-9-yl)oxolan-2-yl]methoxy}(hydroxy)phosphoryl)oxy]phosphonic acid
Traditional Name{[(2R,3S,4R)-3,4-dihydroxy-5-(6-oxo-3H-purin-9-yl)oxolan-2-yl]methoxy(hydroxy)phosphoryl}oxyphosphonic acid
CAS Registry Number86-04-4
SMILES
O[C@@H]1[C@@H](COP(O)(=O)OP(O)(O)=O)OC([C@@H]1O)N1C=NC2=C1NC=NC2=O
InChI Identifier
InChI=1S/C10H14N4O11P2/c15-6-4(1-23-27(21,22)25-26(18,19)20)24-10(7(6)16)14-3-13-5-8(14)11-2-12-9(5)17/h2-4,6-7,10,15-16H,1H2,(H,21,22)(H,11,12,17)(H2,18,19,20)/t4-,6-,7-,10?/m1/s1
InChI KeyJPXZQMKKFWMMGK-VTHZCTBJSA-N
Chemical Taxonomy
Description belongs to the class of organic compounds known as purine ribonucleoside diphosphates. These are purine ribobucleotides with diphosphate group linked to the ribose moiety.
KingdomOrganic compounds
Super ClassNucleosides, nucleotides, and analogues
ClassPurine nucleotides
Sub ClassPurine ribonucleotides
Direct ParentPurine ribonucleoside diphosphates
Alternative Parents
Substituents
  • Purine ribonucleoside diphosphate
  • Purine ribonucleoside monophosphate
  • Pentose phosphate
  • Pentose-5-phosphate
  • Glycosyl compound
  • N-glycosyl compound
  • 6-oxopurine
  • Hypoxanthine
  • Monosaccharide phosphate
  • Organic pyrophosphate
  • Imidazopyrimidine
  • Purine
  • Monoalkyl phosphate
  • Pyrimidone
  • Pyrimidine
  • Alkyl phosphate
  • Phosphoric acid ester
  • Monosaccharide
  • Organic phosphoric acid derivative
  • N-substituted imidazole
  • Tetrahydrofuran
  • Vinylogous amide
  • Azole
  • Imidazole
  • Heteroaromatic compound
  • 1,2-diol
  • Secondary alcohol
  • Organoheterocyclic compound
  • Azacycle
  • Oxacycle
  • Organooxygen compound
  • Organic oxide
  • Organopnictogen compound
  • Organic oxygen compound
  • Organic nitrogen compound
  • Hydrocarbon derivative
  • Organonitrogen compound
  • Alcohol
  • Aromatic heteropolycyclic compound
Molecular FrameworkAromatic heteropolycyclic compounds
External DescriptorsNot Available
Ontology
StatusExpected but not Quantified
Origin
  • Endogenous
BiofunctionNot Available
ApplicationNot Available
Cellular locations
  • Mitochondria
  • Nucleus
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-0.99ALOGPS
logP-3.6ChemAxon
logS-2ALOGPS
pKa (Strongest Acidic)2.65ChemAxon
pKa (Strongest Basic)1.73ChemAxon
Physiological Charge-3ChemAxon
Hydrogen Acceptor Count12ChemAxon
Hydrogen Donor Count6ChemAxon
Polar Surface Area222.26 ŲChemAxon
Rotatable Bond Count6ChemAxon
Refractivity82.64 m³·mol⁻¹ChemAxon
Polarizability33.75 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, Positivesplash10-004j-5921200000-cb3e90eac1de45dd3a4eView in MoNA
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (2 TMS) - 70eV, Positivesplash10-00dj-6196320000-10d043c734c7c3ce7c2aView in MoNA
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (Non-derivatized) - 70eV, PositiveNot AvailableView in JSpectraViewer
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Positivesplash10-000i-0912300000-f3c8f35d649e8697a822View in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Positivesplash10-000i-0900000000-ca4a6257fe76c4c2b1b6View in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Positivesplash10-000i-1900000000-dc3cba7ebcc788b0e4f4View in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Negativesplash10-004r-0901700000-160329f90c3b44108898View in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Negativesplash10-002r-4900000000-0c688018e117d889609eView in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Negativesplash10-004i-9200000000-40b03ca399bfd471c5f4View in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Positivesplash10-000i-0900100000-e46bcfbea9982a491f2fView in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Positivesplash10-000i-0900000000-6648b1702dcbb1355769View in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Positivesplash10-000i-0900000000-341580e528f6c4446ef3View in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Negativesplash10-004i-0003900000-17daa435aa0818f02bb7View in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Negativesplash10-0570-8900000000-d5a169484ed0b980f6c9View in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Negativesplash10-004i-9100000000-a6ce726895863b936073View in MoNA
1D NMR1H NMR Spectrum (1D, 100 MHz, D2O, predicted)Not AvailableView in JSpectraViewer
1D NMR13C NMR Spectrum (1D, 100 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, 1000 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, 200 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, 300 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, 400 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, 500 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, 600 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, 700 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, 800 MHz, D2O, predicted)Not AvailableView in JSpectraViewer
1D NMR1H NMR Spectrum (1D, 900 MHz, D2O, predicted)Not AvailableView in JSpectraViewer
1D NMR13C NMR Spectrum (1D, 900 MHz, D2O, predicted)Not AvailableView in JSpectraViewer
Biological Properties
Cellular Locations
  • Mitochondria
  • Nucleus
Biospecimen LocationsNot Available
Pathways
Normal Concentrations
Not Available
Abnormal Concentrations
Not Available
HMDB IDHMDB0003335
DrugBank IDNot Available
Phenol Explorer Compound IDNot Available
FooDB IDFDB023146
KNApSAcK IDNot Available
Chemspider ID559208
KEGG Compound IDC00104
BioCyc IDNot Available
BiGG ID33869
Wikipedia LinkIDP
METLIN ID6892
PubChem Compound644173
PDB IDNot Available
ChEBI ID17808
References
Synthesis ReferenceTakada, Masao; Kashiwa, Kenichi. Nucleoside 5'-pyrophosphates. Jpn. Tokkyo Koho (1971), 3 pp. CODEN: JAXXAD JP 46021587 19710618 Showa. CAN 75:130076 AN 1971:530076 CAPLUS
Material Safety Data Sheet (MSDS)Not Available
General ReferencesNot Available

Enzymes

Enzyme Details
1. Ectonucleoside triphosphate diphosphohydrolase 8
General function:
Not Available
Specific function:
Canalicular ectonucleoside NTPDase responsible for the main hepatic NTPDase activity. Ectonucleoside NTPDases catalyze the hydrolysis of gamma- and beta-phosphate residues of nucleotides, playing a central role in concentration of extracellular nucleotides. Has activity toward ATP, ADP, UTP and UDP, but not toward AMP (By similarity).
Gene Name:
ENTPD8
Uniprot ID:
A0JND9
Molecular weight:
53240.0
Reactions
IDP + Water → Inosinic acid + Hydrogen phosphatedetails
Inosine triphosphate + Water → IDP + Hydrogen phosphatedetails
Enzyme Details
2. Nucleoside diphosphate kinase 7
General function:
Nucleotide transport and metabolism
Specific function:
Major role in the synthesis of nucleoside triphosphates other than ATP. The ATP gamma phosphate is transferred to the NDP beta phosphate via a ping-pong mechanism, using a phosphorylated active-site intermediate (By similarity).
Gene Name:
NME7
Uniprot ID:
Q5E9Y9
Molecular weight:
42599.0
Reactions
Adenosine triphosphate + IDP → ADP + Inosine triphosphatedetails