P. aeruginosa Metabolome Database: IDP (PAMDB000490)

Identification Taxonomy Physical Properties Biological Properties Spectra Concentrations Links References Enzymes Transporters

Proteins (3280)

Record Information

Version

1.0

Update Date

1/22/2018 11:54:54 AM

Metabolite ID

PAMDB000490

Identification

Name:

IDP

Description:

IDP is an inosine nucleotide containing a pyrophosphate group esterified to the C5 of the sugar moiety.

Structure

🔍MOL SDF PDB SMILES InChI View Structure

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

Average Molecular Weight:

428.1859

Monoisotopic Molecular Weight:

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

Taxonomy Description

This compound belongs to the class of organic compounds known as purine ribonucleoside diphosphates. These are purine ribobucleotides with diphosphate group linked to the ribose moiety.

Kingdom

Organic compounds

Super Class

Nucleosides, nucleotides, and analogues

Class

Purine nucleotides

Sub Class

Purine ribonucleotides

Direct Parent

Purine ribonucleoside diphosphates

Alternative Parents

Substituents

Purine ribonucleoside diphosphate
N-glycosyl compound
Glycosyl compound
Organic pyrophosphate
Monosaccharide phosphate
Hypoxanthine
6-oxopurine
Purine
Imidazopyrimidine
Monoalkyl phosphate
Pyrimidone
Alkyl phosphate
Pyrimidine
Phosphoric acid ester
Organic phosphoric acid derivative
Organic phosphate
N-substituted imidazole
Monosaccharide
Heteroaromatic compound
Vinylogous amide
Oxolane
Imidazole
Azole
Secondary alcohol
1,2-diol
Oxacycle
Azacycle
Organoheterocyclic compound
Hydrocarbon derivative
Organooxygen compound
Organonitrogen compound
Alcohol
Aromatic heteropolycyclic compound

Molecular Framework

Aromatic heteropolycyclic compounds

External Descriptors

Not Available

Physical Properties

State:

Solid

Charge:

-3

Melting point:

Not Available

Experimental Properties:

Property	Value	Source

Predicted Properties

Property	Value	Source
Water Solubility	4.26 mg/mL	ALOGPS
logP	-0.99	ALOGPS
logP	-3.6	ChemAxon
logS	-2	ALOGPS
pKa (Strongest Acidic)	2.65	ChemAxon
pKa (Strongest Basic)	1.73	ChemAxon
Physiological Charge	-3	ChemAxon
Hydrogen Acceptor Count	12	ChemAxon
Hydrogen Donor Count	6	ChemAxon
Polar Surface Area	222.26 Å²	ChemAxon
Rotatable Bond Count	6	ChemAxon
Refractivity	82.64 m³·mol^-1	ChemAxon
Polarizability	33.75 Å³	ChemAxon
Number of Rings	3	ChemAxon
Bioavailability	0	ChemAxon
Rule of Five	Yes	ChemAxon
Ghose Filter	Yes	ChemAxon
Veber's Rule	Yes	ChemAxon
MDDR-like Rule	Yes	ChemAxon

Biological Properties

Cellular Locations:

Cytoplasm

Reactions:

Water + Inosine triphosphate > Hydrogen ion + IDP + Phosphate
Adenosine monophosphate + Inosine triphosphate <> ADP + IDP
Adenosine triphosphate + IDP <> ADP + Inosine triphosphate
Inosine triphosphate + Cytidine <> IDP + Cytidine monophosphate
Inosine triphosphate + Uridine <> IDP + Uridine 5'-monophosphate
Inosine triphosphate + D-Tagatose 6-phosphate <> IDP + D-Tagatose 1,6-bisphosphate

Pathways:

Purine metabolism pae00230

Spectra

Spectra:

Spectrum Type	Description	Splash Key
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Positive	splash10-000i-0912300000-f3c8f35d649e8697a822	View in MoNA
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Positive	splash10-000i-0900000000-ca4a6257fe76c4c2b1b6	View in MoNA
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Positive	splash10-000i-1900000000-dc3cba7ebcc788b0e4f4	View in MoNA
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Negative	splash10-004r-0901700000-160329f90c3b44108898	View in MoNA
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Negative	splash10-002r-4900000000-0c688018e117d889609e	View in MoNA
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Negative	splash10-004i-9200000000-40b03ca399bfd471c5f4	View 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

Links

External Links:

Resource	Link
CHEBI ID	17808
HMDB ID	HMDB03335
Pubchem Compound ID	644173
Kegg ID	C00104
ChemSpider ID	559208
Wikipedia	IDP
BioCyc ID	IDP
EcoCyc ID	IDP

IDP (PAMDB000490)

Structure for IDP (PAMDB000490)