DIDP (ECMDB03536) (M2MDB000509)

IdentificationTaxonomyPhysical PropertiesBiological PropertiesSpectraConcentrationsLinksReferencesEnzymes (2)Transporters (1)XML
Proteins (377)
Record Information
Version2.0
Creation Date2012-05-31 13:59:32 -0600
Update Date2015-06-03 15:54:24 -0600
Secondary Accession Numbers
  • ECMDB03536
Identification
Name:DIDP
DescriptiondIDP (deoxyinoside diphosphate) is a nucleoside. It is an intermediate in purine metabolism. It is converted to dITP or from dITP via multifunctional nucleoside diphosphate kinase and apyrimidinic endonuclease and 3'-phosphodiesterase (EC:2.7.4.6). (KEGG)
Structure
Thumb
MOLSDFPDBSMILESInChI
Synonyms:
  • 2'-Deoxyinosine 5'-diphosphate
  • 2'-Deoxyinosine 5'-diphosphoric acid
  • Deoxyinosine diphosphate
  • Deoxyinosine diphosphoric acid
Chemical Formula:C10H14N4O10P2
Weight:Average: 412.1865
Monoisotopic: 412.018515712
InChI Key:BKUSIKGSPSFQAC-RRKCRQDMSA-N
InChI:InChI=1S/C10H14N4O10P2/c15-5-1-7(14-4-13-8-9(14)11-3-12-10(8)16)23-6(5)2-22-26(20,21)24-25(17,18)19/h3-7,15H,1-2H2,(H,20,21)(H,11,12,16)(H2,17,18,19)/t5-,6+,7+/m0/s1
CAS number:26575-15-5
IUPAC Name:{[hydroxy({[(2R,3S,5R)-3-hydroxy-5-(6-oxo-6,9-dihydro-3H-purin-9-yl)oxolan-2-yl]methoxy})phosphoryl]oxy}phosphonic acid
Traditional IUPAC Name:2'-deoxyinosine
SMILES:O[C@H]1C[C@@H](O[C@@H]1CO[P@@](O)(=O)OP(O)(O)=O)N1C=NC2=C1NC=NC2=O
Chemical Taxonomy
Description belongs to the class of organic compounds known as purine 2'-deoxyribonucleoside diphosphates. These are purine nucleotides with diphosphate group linked to the ribose moiety lacking a hydroxyl group at position 2.
KingdomOrganic compounds
Super ClassNucleosides, nucleotides, and analogues
ClassPurine nucleotides
Sub ClassPurine deoxyribonucleotides
Direct ParentPurine 2'-deoxyribonucleoside diphosphates
Alternative Parents
Substituents
  • Purine 2'-deoxyribonucleoside diphosphate
  • 6-oxopurine
  • Hypoxanthine
  • Organic pyrophosphate
  • Imidazopyrimidine
  • Purine
  • Pyrimidone
  • Monoalkyl phosphate
  • N-substituted imidazole
  • Organic phosphoric acid derivative
  • Phosphoric acid ester
  • Pyrimidine
  • Alkyl phosphate
  • Azole
  • Heteroaromatic compound
  • Vinylogous amide
  • Tetrahydrofuran
  • Imidazole
  • Secondary alcohol
  • Oxacycle
  • Organoheterocyclic compound
  • Azacycle
  • Hydrocarbon derivative
  • Alcohol
  • Organic nitrogen compound
  • Organopnictogen compound
  • Organic oxide
  • Organonitrogen compound
  • Organic oxygen compound
  • Organooxygen compound
  • Aromatic heteropolycyclic compound
Molecular FrameworkAromatic heteropolycyclic compounds
External Descriptors
Physical Properties
State:Liquid
Charge:-3
Melting point:-45.6 °C
Experimental Properties:
PropertyValueSource
Water Solubility:0.00028 mg/mL at 25 oC [YALKOWSKY,SH & DANNENFELSER,RM (1992)]PhysProp
LogP:9.444PhysProp
Predicted Properties
PropertyValueSource
Water Solubility3.62 g/LALOGPS
logP-1ALOGPS
logP-2.7ChemAxon
logS-2.1ALOGPS
pKa (Strongest Acidic)1.73ChemAxon
pKa (Strongest Basic)2.67ChemAxon
Physiological Charge-3ChemAxon
Hydrogen Acceptor Count11ChemAxon
Hydrogen Donor Count5ChemAxon
Polar Surface Area202.03 ŲChemAxon
Rotatable Bond Count6ChemAxon
Refractivity81.13 m³·mol⁻¹ChemAxon
Polarizability33.01 ųChemAxon
Number of Rings3ChemAxon
Bioavailability0ChemAxon
Rule of FiveYesChemAxon
Ghose FilterYesChemAxon
Veber's RuleYesChemAxon
MDDR-like RuleYesChemAxon
Biological Properties
Cellular Locations:Cytoplasm
Reactions:
2'-Deoxyinosine triphosphate + Water > DIDP + Hydrogen ion + Phosphate
Adenosine triphosphate + DIDP <> ADP + 2'-Deoxyinosine triphosphate
SMPDB Pathways:Not Available
KEGG Pathways:
EcoCyc Pathways:Not Available
Concentrations
Not Available
Spectra
Spectra:
Spectrum TypeDescriptionSplash Key
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (Non-derivatized) - 70eV, Positivesplash10-002g-6912000000-07b57ba4fa4eb196ef35View in MoNA
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (1 TMS) - 70eV, Positivesplash10-004m-7912200000-68086875341dd8490f7fView in MoNA
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (Non-derivatized) - 70eV, PositiveNot AvailableView in JSpectraViewer
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (Non-derivatized) - 70eV, PositiveNot AvailableView in JSpectraViewer
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (TMS_1_3) - 70eV, PositiveNot AvailableView in JSpectraViewer
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (TMS_1_4) - 70eV, PositiveNot AvailableView in JSpectraViewer
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (TBDMS_1_1) - 70eV, PositiveNot AvailableView in JSpectraViewer
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (TBDMS_1_3) - 70eV, PositiveNot AvailableView in JSpectraViewer
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (TBDMS_1_4) - 70eV, PositiveNot AvailableView in JSpectraViewer
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS ("dIDP,1TMS,#1" TMS) - 70eV, PositiveNot AvailableView in JSpectraViewer
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Positivesplash10-000i-0901000000-c25470a2b6dd89f05ad9View in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Positivesplash10-000i-0900000000-3d9499d9e41944d634b9View in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Positivesplash10-000i-1900000000-525473dc438b57d3a43dView in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Negativesplash10-03di-0604900000-ed1ddaa7f42a929a87c7View in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Negativesplash10-004r-6900000000-30a416b7228b3caa2d1bView in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Negativesplash10-004i-9100000000-2f4d7cdfeca6c7bfc50cView in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Negativesplash10-03di-0002900000-5bd208fa393222da320cView in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Negativesplash10-004i-9100200000-9e3b234b79a12681e548View in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Negativesplash10-004i-9000000000-83a9083772d3cf547f0cView in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Positivesplash10-000i-0900100000-c91e0c87a55c16b12e0cView in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Positivesplash10-000i-0900000000-b2e36fb98660834d7d24View in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Positivesplash10-000i-0911000000-6110de2395388465a9fdView in MoNA
1D NMR1H NMR SpectrumNot AvailableView in JSpectraViewer
1D NMR13C NMR SpectrumNot AvailableView in JSpectraViewer
1D NMR1H NMR SpectrumNot AvailableView in JSpectraViewer
1D NMR13C NMR SpectrumNot AvailableView in JSpectraViewer
1D NMR1H NMR SpectrumNot AvailableView in JSpectraViewer
1D NMR13C NMR SpectrumNot AvailableView in JSpectraViewer
1D NMR1H NMR SpectrumNot AvailableView in JSpectraViewer
1D NMR13C NMR SpectrumNot AvailableView in JSpectraViewer
1D NMR1H NMR SpectrumNot AvailableView in JSpectraViewer
1D NMR13C NMR SpectrumNot AvailableView in JSpectraViewer
1D NMR1H NMR SpectrumNot AvailableView in JSpectraViewer
1D NMR13C NMR SpectrumNot AvailableView in JSpectraViewer
1D NMR1H NMR SpectrumNot AvailableView in JSpectraViewer
1D NMR13C NMR SpectrumNot AvailableView in JSpectraViewer
1D NMR1H NMR SpectrumNot AvailableView in JSpectraViewer
1D NMR13C NMR SpectrumNot AvailableView in JSpectraViewer
1D NMR1H NMR SpectrumNot AvailableView in JSpectraViewer
1D NMR13C NMR SpectrumNot AvailableView in JSpectraViewer
1D NMR1H NMR SpectrumNot AvailableView in JSpectraViewer
1D NMR13C NMR SpectrumNot AvailableView in JSpectraViewer
References
References:
  • Chantin C, Bonin B, Boulieu R, Bory C: Liquid-chromatographic study of purine metabolism abnormalities in purine nucleoside phosphorylase deficiency. Clin Chem. 1996 Feb;42(2):326-8. Pubmed: 8595732
  • 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:Not Available
Material Safety Data Sheet (MSDS)Not Available
External Links:
ResourceLink
CHEBI ID28823
HMDB IDHMDB03536
Pubchem Compound ID439488
Kegg IDC01344
ChemSpider ID388586
Wikipedia IDDID
BioCyc IDCPD0-2231
EcoCyc IDCPD0-2231

Enzymes

Protein Details
1. Nucleoside diphosphate kinase
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.
Protein Details
2. UPF0244 protein yjjX
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

Protein Details
1. Nucleoside diphosphate kinase
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.