DIMP (ECMDB06555) (M2MDB000681)

IdentificationTaxonomyPhysical PropertiesBiological PropertiesSpectraConcentrationsLinksReferencesEnzymes (5)Transporters (4)XML
Proteins (502)
Record Information
Version2.0
Creation Date2012-05-31 14:08:56 -0600
Update Date2015-06-03 15:54:53 -0600
Secondary Accession Numbers
  • ECMDB06555
Identification
Name:DIMP
DescriptiondIMP is a deoxyribonucleoside and is considered a derivative of the nucleoside inosine, differing from the latter by the replacement of a hydroxyl group (-OH) by hydrogen (-H) at the 2' position of its ribose sugar moiety. The hydrolytic deamination of dAMP residues in DNA yields dIMP residues. The deamination of adenine residues in DNA generates hypoxanthine, which is mutagenic since it can pair not only with thymine but also with cytosine and therefore would result in A-T to G-C transitions after DNA replication. Hypoxanthine DNA glycosylase (EC 3.2.2.15) excises hypoxanthine from DNA containing dIMP residues in cells. (PMID: 10684927, 8016081)
Structure
Thumb
MOLSDFPDBSMILESInChI
Synonyms:
  • 2'-Deoxy-5'-inosinate
  • 2'-Deoxy-5'-inosinic acid
  • 2'-Deoxy-IMP
  • 2'-Deoxyinosine 5'-monophosphate
  • 2'-Deoxyinosine 5'-monophosphoric acid
  • 2'-Deoxyinosine 5'-phosphate
  • 2'-Deoxyinosine 5'-phosphoric acid
  • 9-(2-deoxy-5-O-phosphono-β-D-erythro-pentofuranosyl)-9H-purin-6-ol
  • 9-(2-Deoxy-5-O-phosphono-b-D-erythro-pentofuranosyl)-9H-purin-6-ol
  • 9-(2-Deoxy-5-O-phosphono-b-delta-erythro-pentofuranosyl)-9H-purin-6-ol
  • 9-(2-Deoxy-5-O-phosphono-b-δ-erythro-pentofuranosyl)-9H-purin-6-ol
  • 9-(2-Deoxy-5-O-phosphono-beta-D-erythro-pentofuranosyl)-9H-purin-6-ol
  • 9-(2-Deoxy-5-O-phosphono-beta-delta-erythro-pentofuranosyl)-9H-purin-6-ol
  • 9-(2-Deoxy-5-O-phosphono-β-D-erythro-pentofuranosyl)-9H-purin-6-ol
  • 9-(2-Deoxy-5-O-phosphono-β-δ-erythro-pentofuranosyl)-9H-purin-6-ol
  • Deoxyinosine monophosphate
  • Deoxyinosine monophosphoric acid
  • DIMP
  • Hypoxanthine deoxyriboside
  • [(2R,3S,4R,5R)-3-hydroxy-5-(6-hydroxy-9H-purin-9-yl)tetrahydrofuran-2-yl]methyl dihydrogen phosphate
  • [(2R,3S,4R,5R)-3-Hydroxy-5-(6-hydroxy-9H-purin-9-yl)tetrahydrofuran-2-yl]methyl dihydrogen phosphoric acid
Chemical Formula:C10H13N4O7P
Weight:Average: 332.2066
Monoisotopic: 332.052185302
InChI Key:PHNGFPPXDJJADG-RRKCRQDMSA-N
InChI:InChI=1S/C10H13N4O7P/c15-5-1-7(21-6(5)2-20-22(17,18)19)14-4-13-8-9(14)11-3-12-10(8)16/h3-7,15H,1-2H2,(H,11,12,16)(H2,17,18,19)/t5-,6+,7+/m0/s1
CAS number:3393-18-8
IUPAC Name:{[(2R,3S,5R)-3-hydroxy-5-(6-oxo-6,9-dihydro-3H-purin-9-yl)oxolan-2-yl]methoxy}phosphonic acid
Traditional IUPAC Name:[(2R,3S,5R)-3-hydroxy-5-(6-oxo-3H-purin-9-yl)oxolan-2-yl]methoxyphosphonic acid
SMILES:O[C@H]1C[C@@H](O[C@@H]1COP(O)(O)=O)N1C=NC2=C1NC=NC2=O
Chemical Taxonomy
Description belongs to the class of organic compounds known as purine 2'-deoxyribonucleoside monophosphates. These are purine nucleotides with monophosphate 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 monophosphates
Alternative Parents
Substituents
  • Purine 2'-deoxyribonucleoside monophosphate
  • Hypoxanthine
  • Imidazopyrimidine
  • Purine
  • Hydroxypyrimidine
  • Monoalkyl phosphate
  • N-substituted imidazole
  • Organic phosphoric acid derivative
  • Phosphoric acid ester
  • Pyrimidine
  • Alkyl phosphate
  • Azole
  • Imidazole
  • Heteroaromatic compound
  • Tetrahydrofuran
  • Secondary alcohol
  • Oxacycle
  • Azacycle
  • Organoheterocyclic compound
  • Alcohol
  • Hydrocarbon derivative
  • Organooxygen compound
  • Organonitrogen compound
  • Organic oxide
  • Organopnictogen compound
  • Organic oxygen compound
  • Organic nitrogen compound
  • Aromatic heteropolycyclic compound
Molecular FrameworkAromatic heteropolycyclic compounds
External Descriptors
Physical Properties
State:Solid
Charge:-3
Melting point:Not Available
Experimental Properties:
PropertyValueSource
Predicted Properties
PropertyValueSource
Water Solubility2.1 g/LALOGPS
logP-1.6ALOGPS
logP-2.6ChemAxon
logS-2.2ALOGPS
pKa (Strongest Acidic)1.22ChemAxon
pKa (Strongest Basic)2.77ChemAxon
Physiological Charge-3ChemAxon
Hydrogen Acceptor Count9ChemAxon
Hydrogen Donor Count4ChemAxon
Polar Surface Area155.5 ŲChemAxon
Rotatable Bond Count4ChemAxon
Refractivity70.26 m³·mol⁻¹ChemAxon
Polarizability27.21 ųChemAxon
Number of Rings3ChemAxon
Bioavailability1ChemAxon
Rule of FiveYesChemAxon
Ghose FilterYesChemAxon
Veber's RuleYesChemAxon
MDDR-like RuleYesChemAxon
Biological Properties
Cellular Locations:Cytoplasm
Reactions:
DIMP + Water > Deoxyinosine + Phosphate
2'-Deoxyinosine triphosphate + Water > DIMP + Hydrogen ion + Pyrophosphate
2'-Deoxyinosine triphosphate + Water <> DIMP + Pyrophosphate
Xanthosine 5-triphosphate + Water + 2'-Deoxyinosine triphosphate <> Xanthylic acid + Pyrophosphate + DIMP
SMPDB Pathways:Not Available
KEGG Pathways:
EcoCyc Pathways:Not Available
Concentrations
Not Available
Spectra
Spectra:
Spectrum TypeDescriptionSplash Key
GC-MSGC-MS Spectrum - GC-EI-TOF (Pegasus III TOF-MS system, Leco; GC 6890, Agilent Technologies) (4 TMS)splash10-001i-9210000000-53948c1a90a0f6914597View in MoNA
GC-MSGC-MS Spectrum - GC-EI-TOF (Non-derivatized)splash10-001i-9210000000-53948c1a90a0f6914597View in MoNA
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (Non-derivatized) - 70eV, Positivesplash10-0002-9401000000-3e05abb6a8d8b1a335b6View in MoNA
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (1 TMS) - 70eV, Positivesplash10-00rx-7923000000-8831273c387905273e72View 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 (UPLC Q-Tof Premier, Waters) , Positivesplash10-001r-0619000000-1a0eb2cb24a05602189fView in MoNA
LC-MS/MSLC-MS/MS Spectrum - LC-ESI-QTOF (UPLC Q-Tof Premier, Waters) 30V, Positivesplash10-000i-2902000000-8031212ff8d5a3caf932View in MoNA
LC-MS/MSLC-MS/MS Spectrum - LC-ESI-QTOF (UPLC Q-Tof Premier, Waters) , Negativesplash10-005j-9803000000-e0eccae074a61767e080View in MoNA
LC-MS/MSLC-MS/MS Spectrum - LC-ESI-QTOF , negativesplash10-005j-9803000000-e0eccae074a61767e080View in MoNA
LC-MS/MSLC-MS/MS Spectrum - LC-ESI-QTOF , positivesplash10-001r-0619000000-1a0eb2cb24a05602189fView in MoNA
LC-MS/MSLC-MS/MS Spectrum - LC-ESI-QTOF , positivesplash10-000i-2902000000-8031212ff8d5a3caf932View in MoNA
LC-MS/MSLC-MS/MS Spectrum - 30V, Positivesplash10-000i-2902000000-8031212ff8d5a3caf932View in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Positivesplash10-000i-0901000000-82485bc6f5afd265ffb6View in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Positivesplash10-000i-0900000000-40c3e510e6f14b9c6415View in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Positivesplash10-000i-0900000000-084491e4ef779439c6e7View in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Negativesplash10-003r-5209000000-fe97448e2adad18be4e1View in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Negativesplash10-004r-9400000000-69f08fb1d6025455e334View in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Negativesplash10-004i-9000000000-eaad95f8c8f37f17a06dView in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Positivesplash10-000i-0900000000-b2e36fb98660834d7d24View in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Positivesplash10-000i-0900000000-c7e643ad3fc1ffc399bbView in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Positivesplash10-0019-5900000000-13459080c7272714095dView in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Negativesplash10-003r-9008000000-2805c5fa43654779dc36View in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Negativesplash10-004i-9101000000-bc2b5d6253fd7cf52a89View in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Negativesplash10-004i-9000000000-ee07b6d42071fb27d3f4View in MoNA
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
1D NMR1H NMR SpectrumNot AvailableView in JSpectraViewer
References
References:
  • 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
  • Saparbaev M, Laval J: Excision of hypoxanthine from DNA containing dIMP residues by the Escherichia coli, yeast, rat, and human alkylpurine DNA glycosylases. Proc Natl Acad Sci U S A. 1994 Jun 21;91(13):5873-7. Pubmed: 8016081
  • Saparbaev, M., Mani, J. C., Laval, J. (2000). "Interactions of the human, rat, Saccharomyces cerevisiae and Escherichia coli 3-methyladenine-DNA glycosylases with DNA containing dIMP residues." Nucleic Acids Res 28:1332-1339. Pubmed: 10684927
  • van der Werf, M. J., Overkamp, K. M., Muilwijk, B., Coulier, L., Hankemeier, T. (2007). "Microbial metabolomics: toward a platform with full metabolome coverage." Anal Biochem 370:17-25. Pubmed: 17765195
Synthesis Reference:Ogilvie, Kelvin K.; Slotin, Lewis A. Anhydronucleosides. XI. Synthesis of nucleotides from 8,2'-thioanhydropurine nucleosides. Canadian Journal of Chemistry (1973), 51(14), 2397-405.
Material Safety Data Sheet (MSDS)Not Available
External Links:
ResourceLink
CHEBI ID28806
HMDB IDHMDB06555
Pubchem Compound ID91531
Kegg IDC06196
ChemSpider ID82650
Wikipedia IDDeoxyinosine_monophosphate
BioCyc IDDIMP
EcoCyc IDDIMP
Ligand ExpoOIP

Enzymes

Protein Details
1. Protein ushA
General function:
Involved in hydrolase activity
Specific function:
Degradation of external UDP-glucose to uridine monophosphate and glucose-1-phosphate, which can then be used by the cell
Gene Name:
ushA
Uniprot ID:
P07024
Molecular weight:
60824
Reactions
UDP-sugar + H(2)O = UMP + alpha-D-aldose 1-phosphate.
A 5'-ribonucleotide + H(2)O = a ribonucleoside + phosphate.
Protein Details
2. Multifunctional protein surE
General function:
Involved in hydrolase activity
Specific function:
Nucleotidase with a broad substrate specificity as it can dephosphorylate various ribo- and deoxyribonucleoside 5'- monophosphates and ribonucleoside 3'-monophosphates with highest affinity to 3'-AMP. Also hydrolyzes polyphosphate (exopolyphosphatase activity) with the preference for short-chain- length substrates (P20-25). Might be involved in the regulation of dNTP and NTP pools, and in the turnover of 3'-mononucleotides produced by numerous intracellular RNases (T1, T2, and F) during the degradation of various RNAs. Also plays a significant physiological role in stress-response and is required for the survival of E.coli in stationary growth phase
Gene Name:
surE
Uniprot ID:
P0A840
Molecular weight:
26900
Reactions
A 5'-ribonucleotide + H(2)O = a ribonucleoside + phosphate.
A 3'-ribonucleotide + H(2)O = a ribonucleoside + phosphate.
(Polyphosphate)(n) + H(2)O = (polyphosphate)(n-1) + phosphate.
Protein Details
3. Class B acid phosphatase
General function:
Involved in acid phosphatase activity
Specific function:
Dephosphorylates several organic phosphomonoesters and catalyzes the transfer of low-energy phosphate groups from phosphomonoesters to hydroxyl groups of various organic compounds. Preferentially acts on aryl phosphoesters. Might function as a broad-spectrum dephosphorylating enzyme able to scavenge both 3'- and 5'-nucleotides and also additional organic phosphomonoesters
Gene Name:
aphA
Uniprot ID:
P0AE22
Molecular weight:
26103
Reactions
A phosphate monoester + H(2)O = an alcohol + phosphate.
Protein Details
4. Nucleoside-triphosphatase rdgB
General function:
Involved in hydrolase activity
Specific function:
Hydrolyzes O6 atom-containing purine bases deoxyinosine triphosphate (dITP) and xanthosine triphosphate (XTP) as well as 2'-deoxy-N-6-hydroxylaminopurine triposphate (dHAPTP) to nucleotide monophosphate and pyrophosphate. Probably excludes non- standard purines from DNA precursor pool, preventing thus incorporation into DNA and avoiding chromosomal lesions
Gene Name:
rdgB
Uniprot ID:
P52061
Molecular weight:
21039
Reactions
A nucleoside triphosphate + H(2)O = a nucleotide + diphosphate.
Protein Details
5. 5'-nucleotidase yfbR
General function:
Involved in catalytic activity
Specific function:
Nucleotidase that shows strict specificity toward deoxyribonucleoside 5'-monophosphates and does not dephosphorylate 5'-ribonucleotides or ribonucleoside 3'-monophosphates. Might be involved in the regulation of all dNTP pools in E.coli
Gene Name:
yfbR
Uniprot ID:
P76491
Molecular weight:
22708
Reactions
A 5'-ribonucleotide + H(2)O = a ribonucleoside + phosphate.

Transporters

Protein Details
1. Outer membrane protein N
General function:
Involved in transporter activity
Specific function:
Non-specific porin
Gene Name:
ompN
Uniprot ID:
P77747
Molecular weight:
41220
Protein Details
2. Outer membrane pore protein E
General function:
Involved in transporter activity
Specific function:
Uptake of inorganic phosphate, phosphorylated compounds, and some other negatively charged solutes
Gene Name:
phoE
Uniprot ID:
P02932
Molecular weight:
38922
Protein Details
3. Outer membrane protein F
General function:
Involved in transporter activity
Specific function:
OmpF is a porin that forms passive diffusion pores which allow small molecular weight hydrophilic materials across the outer membrane. It is also a receptor for the bacteriophage T2
Gene Name:
ompF
Uniprot ID:
P02931
Molecular weight:
39333
Protein Details
4. Outer membrane protein C
General function:
Involved in transporter activity
Specific function:
Forms passive diffusion pores which allow small molecular weight hydrophilic materials across the outer membrane
Gene Name:
ompC
Uniprot ID:
P06996
Molecular weight:
40368