ECMDB: IDP (ECMDB03335) (M2MDB000490)

Identification Taxonomy Physical Properties Biological Properties Spectra Concentrations Links References Enzymes (7)Transporters (1)XML

Proteins (1249)

Record Information

Version

2.0

Creation Date

2012-05-31 13:58:31 -0600

Update Date

2015-06-03 15:54:22 -0600

Secondary Accession Numbers

ECMDB03335

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

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.

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
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 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 g/L	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

SMPDB Pathways:

Not Available

KEGG Pathways:

Purine metabolism ec00230

EcoCyc Pathways:

Not Available

Concentrations

Concentration	Strain	Media	Growth Status	Growth System	Temperature	Details
75± 0 uM	BW25113	48 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 Gluco	Stationary Phase, glucose limited	Bioreactor, pH controlled, O2 and CO2 controlled, dilution rate: 0.2/h	37 oC	PMID: 17379776
24± 0 uM	K12 NCM3722	Gutnick 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 glucose	Mid-Log Phase	Shake flask and filter culture	37 oC	PMID: 19561621

Find out more about how we convert literature concentrations.

Spectra

Spectra:

Spectrum Type	Description	Splash Key
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (Non-derivatized) - 70eV, Positive	splash10-004j-5921200000-cb3e90eac1de45dd3a4e	View in MoNA
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (2 TMS) - 70eV, Positive	splash10-00dj-6196320000-10d043c734c7c3ce7c2a	View in MoNA
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (Non-derivatized) - 70eV, Positive	Not Available	View in JSpectraViewer
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
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Positive	splash10-000i-0900100000-e46bcfbea9982a491f2f	View in MoNA
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Positive	splash10-000i-0900000000-6648b1702dcbb1355769	View in MoNA
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Positive	splash10-000i-0900000000-341580e528f6c4446ef3	View in MoNA
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Negative	splash10-004i-0003900000-17daa435aa0818f02bb7	View in MoNA
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Negative	splash10-0570-8900000000-d5a169484ed0b980f6c9	View in MoNA
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Negative	splash10-004i-9100000000-a6ce726895863b936073	View in MoNA
1D NMR	1H NMR Spectrum	Not Available	View in JSpectraViewer
1D NMR	13C NMR Spectrum	Not Available	View in JSpectraViewer
1D NMR	1H NMR Spectrum	Not Available	View in JSpectraViewer
1D NMR	13C NMR Spectrum	Not Available	View in JSpectraViewer
1D NMR	1H NMR Spectrum	Not Available	View in JSpectraViewer
1D NMR	13C NMR Spectrum	Not Available	View in JSpectraViewer
1D NMR	1H NMR Spectrum	Not Available	View in JSpectraViewer
1D NMR	13C NMR Spectrum	Not Available	View in JSpectraViewer
1D NMR	1H NMR Spectrum	Not Available	View in JSpectraViewer
1D NMR	13C NMR Spectrum	Not Available	View in JSpectraViewer
1D NMR	1H NMR Spectrum	Not Available	View in JSpectraViewer
1D NMR	13C NMR Spectrum	Not Available	View in JSpectraViewer
1D NMR	1H NMR Spectrum	Not Available	View in JSpectraViewer
1D NMR	13C NMR Spectrum	Not Available	View in JSpectraViewer
1D NMR	1H NMR Spectrum	Not Available	View in JSpectraViewer
1D NMR	13C NMR Spectrum	Not Available	View in JSpectraViewer
1D NMR	1H NMR Spectrum	Not Available	View in JSpectraViewer
1D NMR	13C NMR Spectrum	Not Available	View in JSpectraViewer
1D NMR	1H NMR Spectrum	Not Available	View in JSpectraViewer
1D NMR	13C NMR Spectrum	Not Available	View in JSpectraViewer

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

Enzymes

Protein Details

1. 6-phosphofructokinase isozyme 2

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.

Protein Details

2. 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

3. 6-phosphofructokinase isozyme 1

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.

Protein Details

4. Uridine kinase

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.

Protein Details

5. Putative ribosome biogenesis GTPase RsgA

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

Protein Details

6. Adenylate kinase

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.

Protein Details

7. 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.

IDP (ECMDB03335) (M2MDB000490)

Structure for #<Compound:0x8176fbfc>

Enzymes

Reactions

Reactions

Reactions

Reactions

Reactions

Reactions

Transporters

Reactions