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Record Information
Version4.0
StatusExpected but not Quantified
Creation Date2006-08-12 18:44:06 UTC
Update Date2020-02-26 21:24:31 UTC
HMDB IDHMDB0003335
Secondary Accession Numbers
  • HMDB03335
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. In humans, IDP is involved in the oncogenic action of 2-hydroxyglutarate.
Structure
Data?1582752271
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
Disposition

Source:

Biological location:

Process

Naturally occurring process:

Physical Properties
StateSolid
Experimental Properties
PropertyValueReference
Melting PointNot AvailableNot Available
Boiling PointNot AvailableNot Available
Water SolubilityNot AvailableNot Available
LogPNot AvailableNot Available
Predicted Properties
PropertyValueSource
Water Solubility4.26 g/LALOGPS
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
BioavailabilityNoChemAxon
Rule of FiveNoChemAxon
Ghose FilterNoChemAxon
Veber's RuleNoChemAxon
MDDR-like RuleYesChemAxon
Spectra
Spectrum TypeDescriptionSplash KeyView
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (Non-derivatized) - 70eV, Positivesplash10-004j-5921200000-cb3e90eac1de45dd3a4eSpectrum
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (2 TMS) - 70eV, Positivesplash10-00dj-6196320000-10d043c734c7c3ce7c2aSpectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Positivesplash10-000i-0912300000-f3c8f35d649e8697a822Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Positivesplash10-000i-0900000000-ca4a6257fe76c4c2b1b6Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Positivesplash10-000i-1900000000-dc3cba7ebcc788b0e4f4Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Negativesplash10-004r-0901700000-160329f90c3b44108898Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Negativesplash10-002r-4900000000-0c688018e117d889609eSpectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Negativesplash10-004i-9200000000-40b03ca399bfd471c5f4Spectrum
Biological Properties
Cellular Locations
  • Extracellular
  • Mitochondria
  • Nucleus
Biospecimen LocationsNot Available
Tissue LocationsNot Available
Pathways
Normal Concentrations
Not Available
Abnormal Concentrations
Not Available
Associated Disorders and Diseases
Disease ReferencesNone
Associated OMIM IDsNone
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
Food Biomarker OntologyNot Available
VMH IDNot Available
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 References
  1. Hlushko LV, Makovets'ka TI, Neiko IeM: [The dynamics of the glycocholic acid content of the bile in patients with chronic inactive hepatitis]. Lik Sprava. 1995 May-Jun;(5-6):152-4. [PubMed:8630789 ]

Only showing the first 10 proteins. There are 31 proteins in total.

Enzymes

General function:
Involved in hydrolase activity
Specific function:
In the nervous system, could hydrolyze ATP and other nucleotides to regulate purinergic neurotransmission. Could also be implicated in the prevention of platelet aggregation by hydrolyzing platelet-activating ADP to AMP. Hydrolyzes ATP and ADP equally well.
Gene Name:
ENTPD1
Uniprot ID:
P49961
Molecular weight:
58706.0
Reactions
Inosine triphosphate + Water → IDP + Phosphatedetails
IDP + Water → Inosinic acid + Phosphatedetails
General function:
Involved in calcium ion binding
Specific function:
Calcium-dependent nucleotidase with a preference for UDP. The order of activity with different substrates is UDP > GDP > UTP > GTP. Has very low activity towards ADP and even lower activity towards ATP. Does not hydrolyze AMP and GMP. Involved in proteoglycan synthesis.
Gene Name:
CANT1
Uniprot ID:
Q8WVQ1
Molecular weight:
44839.24
Reactions
IDP + Water → Inosinic acid + Phosphatedetails
General function:
Involved in hydrolase activity
Specific function:
Has a threefold preference for the hydrolysis of ATP over ADP.
Gene Name:
ENTPD3
Uniprot ID:
O75355
Molecular weight:
59104.76
Reactions
Inosine triphosphate + Water → IDP + Phosphatedetails
IDP + Water → Inosinic acid + Phosphatedetails
General function:
Involved in ATP binding
Specific function:
Phosphorylates uridine and cytidine to uridine monophosphate and cytidine monophosphate. Does not phosphorylate deoxyribonucleosides or purine ribonucleosides. Can use ATP or GTP as a phosphate donor. Can also phosphorylate cytidine and uridine nucleoside analogs such as 6-azauridine, 5-fluorouridine, 4-thiouridine, 5-bromouridine, N(4)-acetylcytidine, N(4)-benzoylcytidine, 5-fluorocytidine, 2-thiocytidine, 5-methylcytidine, and N(4)-anisoylcytidine.
Gene Name:
UCK1
Uniprot ID:
Q9HA47
Molecular weight:
22760.43
Reactions
Inosine triphosphate + Cytidine → IDP + Cytidine monophosphatedetails
Inosine triphosphate + Uridine → IDP + Uridine 5'-monophosphatedetails
General function:
Involved in nucleoside diphosphate kinase activity
Specific function:
Major role in the synthesis of nucleoside triphosphates other than ATP (By similarity).
Gene Name:
NME4
Uniprot ID:
O00746
Molecular weight:
20658.45
Reactions
Adenosine triphosphate + IDP → ADP + Inosine triphosphatedetails
General function:
Involved in nucleoside diphosphate kinase activity
Specific function:
Major role in the synthesis of nucleoside triphosphates other than ATP. Possesses nucleoside-diphosphate kinase, serine/threonine-specific protein kinase, geranyl and farnesyl pyrophosphate kinase, histidine protein kinase and 3'-5' exonuclease activities. Involved in cell proliferation, differentiation and development, signal transduction, G protein-coupled receptor endocytosis, and gene expression. Required for neural development including neural patterning and cell fate determination.
Gene Name:
NME1
Uniprot ID:
P15531
Molecular weight:
17148.635
Reactions
Adenosine triphosphate + IDP → ADP + Inosine triphosphatedetails
General function:
Involved in nucleoside diphosphate kinase activity
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.
Gene Name:
NME7
Uniprot ID:
Q9Y5B8
Molecular weight:
42491.365
Reactions
Adenosine triphosphate + IDP → ADP + Inosine triphosphatedetails
General function:
Involved in nucleoside diphosphate kinase activity
Specific function:
Major role in the synthesis of nucleoside triphosphates other than ATP. Negatively regulates Rho activity by interacting with AKAP13/LBC. Acts as a transcriptional activator of the MYC gene; binds DNA non-specifically (PubMed:8392752). Exhibits histidine protein kinase activity.
Gene Name:
NME2
Uniprot ID:
P22392
Molecular weight:
30136.92
Reactions
Adenosine triphosphate + IDP → ADP + Inosine triphosphatedetails
General function:
Involved in nucleoside diphosphate kinase activity
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. Probably has a role in normal hematopoiesis by inhibition of granulocyte differentiation and induction of apoptosis.
Gene Name:
NME3
Uniprot ID:
Q13232
Molecular weight:
19014.85
Reactions
Adenosine triphosphate + IDP → ADP + Inosine triphosphatedetails
General function:
Involved in nucleoside diphosphate kinase activity
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. Inhibitor of p53-induced apoptosis.
Gene Name:
NME6
Uniprot ID:
O75414
Molecular weight:
22002.965
Reactions
Adenosine triphosphate + IDP → ADP + Inosine triphosphatedetails

Only showing the first 10 proteins. There are 31 proteins in total.