Record Information
Version2.0
Creation Date2012-05-31 13:58:31 -0600
Update Date2015-06-03 15:54:22 -0600
Secondary Accession Numbers
  • ECMDB03335
Identification
Name:IDP
DescriptionIDP is an inosine nucleotide containing a pyrophosphate group esterified to the C5 of the sugar moiety.
Structure
Thumb
Synonyms:
  • 5'-IDP
  • IDP
  • Inosine 5'-(trihydrogen diphosphate)
  • Inosine 5'-(trihydrogen diphosphoric acid)
  • Inosine 5'-(trihydrogen pyrophosphate)
  • Inosine 5'-(trihydrogen pyrophosphoric acid)
  • Inosine 5'-diphosphate
  • Inosine 5'-diphosphoric acid
  • Inosine 5'-pyrophosphate
  • Inosine 5'-pyrophosphoric acid
  • Inosine diphosphate
  • Inosine diphosphoric acid
  • Inosine pyrophosphate
  • Inosine pyrophosphoric acid
  • Riboxin
  • Riboxine
Chemical Formula:C10H14N4O11P2
Weight:Average: 428.1859
Monoisotopic: 428.013430334
InChI Key:JPXZQMKKFWMMGK-VTHZCTBJSA-N
InChI: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
CAS number:86-04-4
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 IUPAC Name:{[(2R,3S,4R)-3,4-dihydroxy-5-(6-oxo-3H-purin-9-yl)oxolan-2-yl]methoxy(hydroxy)phosphoryl}oxyphosphonic acid
SMILES:O[C@@H]1[C@@H](COP(O)(=O)OP(O)(O)=O)OC([C@@H]1O)N1C=NC2=C1NC=NC2=O
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
Physical Properties
State:Solid
Charge:-3
Melting point:Not Available
Experimental Properties:
PropertyValueSource
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
Bioavailability0ChemAxon
Rule of FiveYesChemAxon
Ghose FilterYesChemAxon
Veber's RuleYesChemAxon
MDDR-like RuleYesChemAxon
Biological Properties
Cellular Locations:Cytoplasm
Reactions:
SMPDB Pathways:Not Available
KEGG Pathways:
EcoCyc Pathways:Not Available
Concentrations
ConcentrationStrainMediaGrowth StatusGrowth SystemTemperatureDetails
75± 0 uMBW2511348 mM Na2HPO4, 22 mM KH2PO4, 10 mM NaCl, 45 mM (NH4)2SO4, supplemented with 1 mM MgSO4, 1 mg/l thiamine·HCl, 5.6 mg/l CaCl2, 8 mg/l FeCl3, 1 mg/l MnCl2·4H2O, 1.7 mg/l ZnCl2, 0.43 mg/l CuCl2·2H2O, 0.6 mg/l CoCl2·2H2O and 0.6 mg/l Na2MoO4·2H2O. 4 g/L GlucoStationary Phase, glucose limitedBioreactor, pH controlled, O2 and CO2 controlled, dilution rate: 0.2/h37 oCPMID: 17379776
24± 0 uMK12 NCM3722Gutnick minimal complete medium (4.7 g/L KH2PO4; 13.5 g/L K2HPO4; 1 g/L K2SO4; 0.1 g/L MgSO4-7H2O; 10 mM NH4Cl) with 4 g/L glucoseMid-Log PhaseShake flask and filter culture37 oCPMID: 19561621
Find out more about how we convert literature concentrations.
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 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
References
References:
  • Bennett, B. D., Kimball, E. H., Gao, M., Osterhout, R., Van Dien, S. J., Rabinowitz, J. D. (2009). "Absolute metabolite concentrations and implied enzyme active site occupancy in Escherichia coli." Nat Chem Biol 5:593-599. Pubmed: 19561621
  • 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
  • Ishii, N., Nakahigashi, K., Baba, T., Robert, M., Soga, T., Kanai, A., Hirasawa, T., Naba, M., Hirai, K., Hoque, A., Ho, P. Y., Kakazu, Y., Sugawara, K., Igarashi, S., Harada, S., Masuda, T., Sugiyama, N., Togashi, T., Hasegawa, M., Takai, Y., Yugi, K., Arakawa, K., Iwata, N., Toya, Y., Nakayama, Y., Nishioka, T., Shimizu, K., Mori, H., Tomita, M. (2007). "Multiple high-throughput analyses monitor the response of E. coli to perturbations." Science 316:593-597. Pubmed: 17379776
  • Kanehisa, M., Goto, S., Sato, Y., Furumichi, M., Tanabe, M. (2012). "KEGG for integration and interpretation of large-scale molecular data sets." Nucleic Acids Res 40:D109-D114. Pubmed: 22080510
  • Keseler, I. M., Collado-Vides, J., Santos-Zavaleta, A., Peralta-Gil, M., Gama-Castro, S., Muniz-Rascado, L., Bonavides-Martinez, C., Paley, S., Krummenacker, M., Altman, T., Kaipa, P., Spaulding, A., Pacheco, J., Latendresse, M., Fulcher, C., Sarker, M., Shearer, A. G., Mackie, A., Paulsen, I., Gunsalus, R. P., Karp, P. D. (2011). "EcoCyc: a comprehensive database of Escherichia coli biology." Nucleic Acids Res 39:D583-D590. Pubmed: 21097882
Synthesis Reference:Takada, 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
External Links:
ResourceLink
CHEBI ID17808
HMDB IDHMDB03335
Pubchem Compound ID644173
Kegg IDC00104
ChemSpider ID559208
WikipediaIDP
BioCyc IDIDP
EcoCyc IDIDP

Enzymes

General function:
Involved in phosphotransferase activity, alcohol group as acceptor
Specific function:
ATP + D-fructose 6-phosphate = ADP + D- fructose 1,6-bisphosphate
Gene Name:
pfkB
Uniprot ID:
P06999
Molecular weight:
32456
Reactions
ATP + D-fructose 6-phosphate = ADP + D-fructose 1,6-bisphosphate.
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:
ndk
Uniprot ID:
P0A763
Molecular weight:
15463
Reactions
ATP + nucleoside diphosphate = ADP + nucleoside triphosphate.
General function:
Involved in ATP binding
Specific function:
ATP + D-fructose 6-phosphate = ADP + D- fructose 1,6-bisphosphate
Gene Name:
pfkA
Uniprot ID:
P0A796
Molecular weight:
34842
Reactions
ATP + D-fructose 6-phosphate = ADP + D-fructose 1,6-bisphosphate.
General function:
Involved in ATP binding
Specific function:
ATP + uridine = ADP + UMP
Gene Name:
udk
Uniprot ID:
P0A8F4
Molecular weight:
24353
Reactions
ATP + uridine = ADP + UMP.
ATP + cytidine = ADP + CMP.
General function:
Involved in GTPase activity
Specific function:
May play a role in 30S ribosomal subunit biogenesis. Unusual circulary permuted GTPase that catalyzes rapid hydrolysis of GTP with a slow catalytic turnover. Dispensible for viability, but important for overall fitness. The intrinsic GTPase activity is stimulated by the presence of 30S (160-fold increase in kcat) or 70S (96 fold increase in kcat) ribosomes (PubMed:14973029). The GTPase is inhibited by aminoglycoside antibiotics such as neomycin and paromycin (PubMed:15466596) streptomycin and spectinomycin (PubMed:15828870). This inhibition is not due to competition for binding sites on the 30S or 70S ribosome (PubMed:15828870)
Gene Name:
rsgA
Uniprot ID:
P39286
Molecular weight:
39193
General function:
Involved in ATP binding
Specific function:
Catalyzes the reversible transfer of the terminal phosphate group between ATP and AMP. This small ubiquitous enzyme involved in the energy metabolism and nucleotide synthesis, is essential for maintenance and cell growth
Gene Name:
adk
Uniprot ID:
P69441
Molecular weight:
23586
Reactions
ATP + AMP = 2 ADP.
General function:
Involved in nucleoside-triphosphatase activity
Specific function:
Specific function unknown
Gene Name:
yjjX
Uniprot ID:
P39411
Molecular weight:
18213
Reactions
A nucleoside triphosphate + H(2)O = a nucleoside diphosphate + monophosphate.

Transporters

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:
ndk
Uniprot ID:
P0A763
Molecular weight:
15463
Reactions
ATP + nucleoside diphosphate = ADP + nucleoside triphosphate.