5-Diphosphoinositol pentakisphosphate (YMDB00013)

Identification

YMDB ID

YMDB00013

Name

5-Diphosphoinositol pentakisphosphate

Species

Saccharomyces cerevisiae

Strain

Baker's yeast

Description

5-Diphosphoinositol pentakisphosphate, also known as 5-PP-insp5 or 5beta-ip7, belongs to the class of organic compounds known as inositol phosphates. Inositol phosphates are compounds containing a phosphate group attached to an inositol (or cyclohexanehexol) moiety. 5-Diphosphoinositol pentakisphosphate is an extremely strong acidic compound (based on its pKa). 5-Diphosphoinositol pentakisphosphate exists in all eukaryotes, ranging from yeast to humans. Within yeast, 5-diphosphoinositol pentakisphosphate participates in a number of enzymatic reactions. In particular, 5-diphosphoinositol pentakisphosphate can be biosynthesized from myo-inositol hexakisphosphate; which is mediated by the enzyme inositol hexakisphosphate kinase 1. In addition, 5-diphosphoinositol pentakisphosphate can be converted into myo-inositol hexakisphosphate; which is catalyzed by the enzyme inositol polyphosphate kinase. In yeast, 5-diphosphoinositol pentakisphosphate is involved in the metabolic pathway called the inositol phosphate metabolism pathway.

Structure

MOL SDF PDB SMILES InChI

Synonyms

(1R,2R,3S,4S,5R,6S)-2,3,4,5,6-Pentakis(phosphonooxy)cyclohexyl trihydrogen diphosphate
(1R,2R,3S,4S,5R,6S)-2,3,4,5,6-Pentakis(phosphonooxy)cyclohexyl trihydrogen diphosphoric acid
1,2,3,4,6-pentakis-O-phosphono-1D-myo-inositol 5-(trihydrogen diphosphate)
1D-myo-Inositol 5-diphosphate 1,2,3,4,6-pentakisphosphate
1D-myo-inositol 5-diphosphate pentakisphosphate
1D-myo-Inositol 5-diphosphoric acid 1,2,3,4,6-pentakisphosphoric acid
1D-myo-Inositol 5-diphosphoric acid pentakisphosphoric acid
5-Diphospho-1D-myo-inositol 1,2,3,4,6-pentakisphosphate
5-diphospho-1D-myo-inositol pentakisphosphate
5-Diphosphoinositol pentakisphosphoric acid
5-PP-InsP5
5beta 5PP-IP5
5beta-IP7
diphosphoinositol pentakisphosphate
InsP7
IP7
PP-InsP5
myo-Inositol 1,2,3,4,6-pentakis(dihydrogen phosphate) 5-(trihydrogen diphosphate)

CAS number

149714-25-0

Weight

Average: 740.0152
Monoisotopic: 739.827700986

InChI Key

UPHPWXPNZIOZJL-KXXVROSKSA-N

InChI

InChI=1S/C6H19O27P7/c7-34(8,9)27-1-2(28-35(10,11)12)4(30-37(16,17)18)6(32-40(25,26)33-39(22,23)24)5(31-38(19,20)21)3(1)29-36(13,14)15/h1-6H,(H,25,26)(H2,7,8,9)(H2,10,11,12)(H2,13,14,15)(H2,16,17,18)(H2,19,20,21)(H2,22,23,24)/t1-,2+,3-,4-,5+,6+

IUPAC Name

{[(1R,2r,3S,4R,5s,6S)-2-{[hydroxy(phosphonooxy)phosphoryl]oxy}-3,4,5,6-tetrakis(phosphonooxy)cyclohexyl]oxy}phosphonic acid

Traditional IUPAC Name

[(1R,2r,3S,4R,5s,6S)-2-{[hydroxy(phosphonooxy)phosphoryl]oxy}-3,4,5,6-tetrakis(phosphonooxy)cyclohexyl]oxyphosphonic acid

Chemical Formula

C₆H₁₉O₂₇P₇

SMILES

[H]OP(=O)(O[H])O[C@]1([H])[C@]([H])(OP(=O)(O[H])O[H])[C@@]([H])(OP(=O)(O[H])O[H])[C@]([H])(OP(=O)(O[H])OP(=O)(O[H])O[H])[C@@]([H])(OP(=O)(O[H])O[H])[C@]1([H])OP(=O)(O[H])O[H]

Chemical Taxonomy

Description

belongs to the class of organic compounds known as inositol phosphates. Inositol phosphates are compounds containing a phosphate group attached to an inositol (or cyclohexanehexol) moiety.

Kingdom

Organic compounds

Super Class

Organic oxygen compounds

Class

Organooxygen compounds

Sub Class

Alcohols and polyols

Direct Parent

Inositol phosphates

Alternative Parents

Substituents

Inositol phosphate
Organic pyrophosphate
Monoalkyl phosphate
Alkyl phosphate
Phosphoric acid ester
Organic phosphoric acid derivative
Organic oxide
Hydrocarbon derivative
Aliphatic homomonocyclic compound

Molecular Framework

Aliphatic homomonocyclic compounds

External Descriptors

myo-inositol pentakisphosphate (CHEBI:30164 )

Physical Properties

State

Solid

Charge

Melting point

Not Available

Experimental Properties

Property	Value	Reference
Water Solubility	Not Available	PhysProp
LogP	Not Available	PhysProp

Predicted Properties

Property	Value	Source
Water Solubility	14 g/L	ALOGPS
logP	0.35	ALOGPS
logP	-4.9	ChemAxon
logS	-1.7	ALOGPS
pKa (Strongest Acidic)	0.14	ChemAxon
Physiological Charge	-12	ChemAxon
Hydrogen Acceptor Count	20	ChemAxon
Hydrogen Donor Count	13	ChemAxon
Polar Surface Area	447.09 Å²	ChemAxon
Rotatable Bond Count	14	ChemAxon
Refractivity	111.89 m³·mol⁻¹	ChemAxon
Polarizability	46.86 Å³	ChemAxon
Number of Rings	1	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

Organoleptic Properties

Not Available

SMPDB Pathways

Inositol phosphate metabolism

PW002495

KEGG Pathways

Inositol phosphate metabolism

ec00562

SMPDB Reactions

KEGG Reactions

Concentrations

Intracellular Concentrations

Not Available

Extracellular Concentrations

Not Available

Spectra

Spectrum Type	Description	Splash Key	View
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (Non-derivatized) - 70eV, Positive	splash10-056v-3500129000-92e02f48f80539fd2ebb	JSpectraViewer
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Positive	splash10-01ox-2200039500-ca3324ec34611cb741e8	JSpectraViewer
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Positive	splash10-01ox-1100019100-a4bf41f87596bb42e4aa	JSpectraViewer
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Positive	splash10-03dl-3200592000-718743d53ee9b1a54936	JSpectraViewer
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Negative	splash10-002r-4100001900-58fc5d06ef574febc5fc	JSpectraViewer
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Negative	splash10-056r-9300013300-99dcc5e94c530a9c5edd	JSpectraViewer
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Negative	splash10-004i-9000000000-7891e87bda74c3a75d76	JSpectraViewer
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Negative	splash10-000i-0000000900-4db44a159198f14597ed	JSpectraViewer
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Negative	splash10-00bi-5000001900-ae421193acbffe665198	JSpectraViewer
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Negative	splash10-004i-9100013000-12bcf1f710fd737c956b	JSpectraViewer
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Positive	splash10-0006-0000000900-93209a4c8cd3c7e5e96b	JSpectraViewer
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Positive	splash10-03dl-0000009500-e5f85269addd70fd0c57	JSpectraViewer
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Positive	splash10-01q9-0000950000-7df113ce88ed8658d548	JSpectraViewer
1D NMR	13C NMR Spectrum	Not Available	JSpectraViewer
1D NMR	1H NMR Spectrum	Not Available	JSpectraViewer
1D NMR	13C NMR Spectrum	Not Available	JSpectraViewer
1D NMR	1H NMR Spectrum	Not Available	JSpectraViewer
1D NMR	13C NMR Spectrum	Not Available	JSpectraViewer
1D NMR	1H NMR Spectrum	Not Available	JSpectraViewer
1D NMR	13C NMR Spectrum	Not Available	JSpectraViewer
1D NMR	1H NMR Spectrum	Not Available	JSpectraViewer
1D NMR	13C NMR Spectrum	Not Available	JSpectraViewer
1D NMR	1H NMR Spectrum	Not Available	JSpectraViewer
1D NMR	13C NMR Spectrum	Not Available	JSpectraViewer
1D NMR	1H NMR Spectrum	Not Available	JSpectraViewer
1D NMR	13C NMR Spectrum	Not Available	JSpectraViewer
1D NMR	1H NMR Spectrum	Not Available	JSpectraViewer
1D NMR	13C NMR Spectrum	Not Available	JSpectraViewer
1D NMR	1H NMR Spectrum	Not Available	JSpectraViewer
1D NMR	13C NMR Spectrum	Not Available	JSpectraViewer
1D NMR	1H NMR Spectrum	Not Available	JSpectraViewer
1D NMR	13C NMR Spectrum	Not Available	JSpectraViewer
1D NMR	1H NMR Spectrum	Not Available	JSpectraViewer

References

References:

UniProt Consortium (2011). "Ongoing and future developments at the Universal Protein Resource." Nucleic Acids Res 39:D214-D219.21051339
Scheer, M., Grote, A., Chang, A., Schomburg, I., Munaretto, C., Rother, M., Sohngen, C., Stelzer, M., Thiele, J., Schomburg, D. (2011). "BRENDA, the enzyme information system in 2011." Nucleic Acids Res 39:D670-D676.21062828
Herrgard, M. J., Swainston, N., Dobson, P., Dunn, W. B., Arga, K. Y., Arvas, M., Bluthgen, N., Borger, S., Costenoble, R., Heinemann, M., Hucka, M., Le Novere, N., Li, P., Liebermeister, W., Mo, M. L., Oliveira, A. P., Petranovic, D., Pettifer, S., Simeonidis, E., Smallbone, K., Spasic, I., Weichart, D., Brent, R., Broomhead, D. S., Westerhoff, H. V., Kirdar, B., Penttila, M., Klipp, E., Palsson, B. O., Sauer, U., Oliver, S. G., Mendes, P., Nielsen, J., Kell, D. B. (2008). "A consensus yeast metabolic network reconstruction obtained from a community approach to systems biology." Nat Biotechnol 26:1155-1160.18846089
Smolka, M. B., Albuquerque, C. P., Chen, S. H., Zhou, H. (2007). "Proteome-wide identification of in vivo targets of DNA damage checkpoint kinases." Proc Natl Acad Sci U S A 104:10364-10369.17563356
Mulugu, S., Bai, W., Fridy, P. C., Bastidas, R. J., Otto, J. C., Dollins, D. E., Haystead, T. A., Ribeiro, A. A., York, J. D. (2007). "A conserved family of enzymes that phosphorylate inositol hexakisphosphate." Science 316:106-109.17412958
Dubois, E., Scherens, B., Vierendeels, F., Ho, M. M., Messenguy, F., Shears, S. B. (2002). "In Saccharomyces cerevisiae, the inositol polyphosphate kinase activity of Kcs1p is required for resistance to salt stress, cell wall integrity, and vacuolar morphogenesis." J Biol Chem 277:23755-23763.11956213
Lee, Y. S., Mulugu, S., York, J. D., O'Shea, E. K. (2007). "Regulation of a cyclin-CDK-CDK inhibitor complex by inositol pyrophosphates." Science 316:109-112.17412959
Gruhler, A., Olsen, J. V., Mohammed, S., Mortensen, P., Faergeman, N. J., Mann, M., Jensen, O. N. (2005). "Quantitative phosphoproteomics applied to the yeast pheromone signaling pathway." Mol Cell Proteomics 4:310-327.15665377
Albuquerque, C. P., Smolka, M. B., Payne, S. H., Bafna, V., Eng, J., Zhou, H. (2008). "A multidimensional chromatography technology for in-depth phosphoproteome analysis." Mol Cell Proteomics 7:1389-1396.18407956
Huh, W. K., Falvo, J. V., Gerke, L. C., Carroll, A. S., Howson, R. W., Weissman, J. S., O'Shea, E. K. (2003). "Global analysis of protein localization in budding yeast." Nature 425:686-691.14562095
Safrany, S. T., Ingram, S. W., Cartwright, J. L., Falck, J. R., McLennan, A. G., Barnes, L. D., Shears, S. B. (1999). "The diadenosine hexaphosphate hydrolases from Schizosaccharomyces pombe and Saccharomyces cerevisiae are homologues of the human diphosphoinositol polyphosphate phosphohydrolase. Overlapping substrate specificities in a MutT-type protein." J Biol Chem 274:21735-21740.10419486
Li, X., Gerber, S. A., Rudner, A. D., Beausoleil, S. A., Haas, W., Villen, J., Elias, J. E., Gygi, S. P. (2007). "Large-scale phosphorylation analysis of alpha-factor-arrested Saccharomyces cerevisiae." J Proteome Res 6:1190-1197.17330950

Synthesis Reference:

Not Available

External Links:

Resource	Link
CHEBI ID	30164
HMDB ID	HMDB06229
Pubchem Compound ID	443247
Kegg ID	C11526
ChemSpider ID	23107121
FOODB ID	FDB023849
Wikipedia ID	Not Available
BioCyc ID	5-DIPHOSPHO-1D-MYO-INOSITOL-12346P

Enzymes

Protein Details

1. Inositol polyphosphate multikinase

General function:: Involved in inositol trisphosphate 3-kinase activity
Specific function:: Has kinase activity and phosphorylates inositol-1,4,5- trisphosphate (Ins(1,4,5)P3) and inositol-1,3,4,5- tetrakisphosphate (Ins(1,3,4,5)P4). Has low kinase activity towards InsP6. Originally it was proposed that the ARGRI and ARGRIII proteins are more likely to be involved in the control of ARGRII activity
Gene Name:: ARG82
Uniprot ID:: P07250
Molecular weight:: 40352.5

Reactions

ATP + 1D-myo-inositol 1,4,5-trisphosphate → ADP + 1D-myo-inositol 1,4,5,6-tetrakisphosphate.
ATP + 1D-myo-inositol 1,4,5,6-tetrakisphosphate → ADP + 1D-myo-inositol 1,3,4,5,6-pentakisphosphate.

Protein Details

2. Diphosphoinositol polyphosphate phosphohydrolase DDP1

General function:: Involved in hydrolase activity
Specific function:: May eliminate potentially toxic dinucleoside polyphosphates during sporulation. Most active against diadenosine 5',5'''-P1,P6-hexaphosphate (Ap6A). Can also hydrolyze diadenosine 5',5'''-P1,P5-pentaphosphate (Ap5A), adenosine 5'-pentaphosphate, and adenosine 5'-tetraphosphate are also substrates, but not diadenosine 5',5'''-P1,P4-tetraphosphate (Ap4A) or other dinucleotides, mononucleotides, nucleotide sugars, or nucleotide alcohols. Also cleaves a beta-phosphate from the diphosphate groups in PP-InsP5 (diphosphoinositol pentakisphosphate) and [PP]2-InsP4 (bisdiphosphoinositol tetrakisphosphate)
Gene Name:: DDP1
Uniprot ID:: Q99321
Molecular weight:: 21572.30078

Reactions

Diphospho-myo-inositol polyphosphate + H(2)O → myo-inositol polyphosphate + phosphate.

Protein Details

3. Inositol hexakisphosphate kinase 1

General function:: Involved in inositol trisphosphate 3-kinase activity
Specific function:: Converts inositol hexakisphosphate (InsP6) to diphosphoinositol pentakisphosphate (InsP7/PP-InsP5). Involved in phosphate regulation and polyphosphate accumulation. Required for resistance to salt stress, cell wall integrity, vacuole morphogenesis, and telomere maintenance
Gene Name:: KCS1
Uniprot ID:: Q12494
Molecular weight:: 119549.0

Reactions

ATP + 1D-myo-inositol hexakisphosphate → ADP + 5-diphospho-1D-myo-inositol (1,2,3,4,6)pentakisphosphate.
ATP + 1D-myo-inositol 1,3,4,5,6-pentakisphosphate → ADP + diphospho-1D-myo-inositol tetrakisphosphate (isomeric configuration unknown).

Protein Details

4. Inositol hexakisphosphate and diphosphoinositol-pentakisphosphate kinase

General function:: Involved in acid phosphatase activity
Specific function:: Bifunctional inositol kinase that catalyzes the formation of diphosphoinositol pentakisphosphate (InsP7 or PP- InsP5) and bi-diphosphoinositol tetrakisphosphate (InsP8 or PP2- InsP4). Converts inositolitol hexakisphosphate (InsP6) to InsP7. Also able to convert InsP7 to InsP8. Probably specifically mediates the formation of 4PP-InsP5 and 6PP-InsP5 InsP7 isomers but not of 5PP-IP5 InsP7 isomer. Required for maintaining celllular integrity, normal growth and interactions with the ARP complex. Acts as a regulator of the PHO80-PHO85 cyclin/cyclin-dependent kinase (CDK) complex, thereby regulating signaling of phosphate availability. Required for the function of the cortical actin cytoskeleton, possibly by participating in correct F-actin localization and ensuring polarized growth
Gene Name:: VIP1
Uniprot ID:: Q06685
Molecular weight:: 129754.0

Reactions

ATP + 1D-myo-inositol hexakisphosphate → ADP + 5-diphospho-1D-myo-inositol (1,2,3,4,6)pentakisphosphate.
ATP + 1D-myo-inositol 1,3,4,5,6-pentakisphosphate → ADP + diphospho-1D-myo-inositol tetrakisphosphate (isomeric configuration unknown).
ATP + 1D-myo-inositol 5-diphosphate pentakisphosphate → ADP + 1D-myo-inositol bisdiphosphate tetrakisphosphate (isomeric configuration unknown).

Protein Details

5. Inositol-pentakisphosphate 2-kinase

General function:: Involved in ATP binding
Specific function:: Has kinase activity and phosphorylates inositol- 1,3,4,5,6-pentakisphosphate (Ins(1,3,4,5,6)P5) to produce 1,2,3,4,5,6-hexakisphosphate (InsP6), also known as phytate
Gene Name:: IPK1
Uniprot ID:: Q06667
Molecular weight:: 32917.69922

Reactions

ATP + 1D-myo-inositol 1,3,4,5,6-pentakisphosphate → ADP + 1D-myo-inositol hexakisphosphate.

5-Diphosphoinositol pentakisphosphate (YMDB00013)

Structure for #<Compound:0xac735300>

Enzymes

Reactions

Reactions

Reactions

Reactions

Reactions