Structure of PDB 5dgi Chain A Binding Site BS02

Receptor Information
>5dgi Chain A (length=318) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
RQIVVGICSMAKKSKSKPMKEILERISLFKYITVVVFEEEVILNEPVENW
PLCDCLISFHSKGFPLDKAVAYAKLRNPFVINDLNMQYLIQDRREVYSIL
QAEGILLPRYAILNRDPNNPKECNLIEGEDHVEVNGEVFQKPFVEKPVSA
EDHNVYIYYPTSAGGGSQRLFRKIGSRSSVYSPESNVRKTGSYIYEEFMP
TDGTDVKVYTVGPDYAHAEARKSPALDGKVERDSEGKEVRYPVILNAREK
LIAWKVCLAFKQTVCGFDLLRANGQSYVCDVNGFSFVKNSMKYYDDCAKI
LGNIVMRELAPQFHIPWS
Ligand information
Ligand ID5A2
InChIInChI=1S/C8H24O28P8/c9-37(10,11)1-39(15,16)31-3-5(33-41(19,20)21)4(32-40(17,18)2-38(12,13)14)7(35-43(25,26)27)8(36-44(28,29)30)6(3)34-42(22,23)24/h3-8H,1-2H2,(H,15,16)(H,17,18)(H2,9,10,11)(H2,12,13,14)(H2,19,20,21)(H2,22,23,24)(H2,25,26,27)(H2,28,29,30)/t3-,4+,5-,6-,7-,8-/m1/s1
InChIKeyWDYISGXURTYYJP-XAZAIFFQSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.9.2C(P(=O)(O)O)P(=O)(O)O[C@@H]1[C@H](C([C@@H]([C@@H](C1OP(=O)(O)O)OP(=O)(CP(=O)(O)O)O)OP(=O)(O)O)OP(=O)(O)O)OP(=O)(O)O
ACDLabs 12.01C1(C(C(C(C(C1OP(O)(O)=O)OP(O)(CP(O)(O)=O)=O)OP(O)(=O)O)OP(CP(O)(O)=O)(=O)O)OP(O)(=O)O)OP(O)(O)=O
CACTVS 3.385O[P](O)(=O)C[P](O)(=O)O[CH]1[CH](O[P](O)(O)=O)[CH](O[P](O)(O)=O)[CH](O[P](O)(O)=O)[CH](O[P](O)(=O)C[P](O)(O)=O)[CH]1O[P](O)(O)=O
CACTVS 3.385O[P](O)(=O)C[P](O)(=O)O[C@@H]1[C@@H](O[P](O)(O)=O)[C@H](O[P](O)(O)=O)[C@H](O[P](O)(O)=O)[C@H](O[P](O)(=O)C[P](O)(O)=O)[C@H]1O[P](O)(O)=O
OpenEye OEToolkits 1.9.2C(P(=O)(O)O)P(=O)(O)OC1C(C(C(C(C1OP(=O)(O)O)OP(=O)(O)O)OP(=O)(O)O)OP(=O)(CP(=O)(O)O)O)OP(=O)(O)O
FormulaC8 H24 O28 P8
Name3,5-di-methylenebisphosphonate inositol tetrakisphosphate;
{[(1R,3S,4R,5S,6R)-2,4,5,6-tetrakis(phosphonooxy)cyclohexane-1,3-diyl]bis[oxy(hydroxyphosphoryl)methanediyl]}bis(phosphonic acid)
ChEMBL
DrugBank
ZINCZINC000584904974
PDB chain5dgi Chain A Residue 402 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
Global viewLocal viewStructure summary

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PDB5dgi Cellular Cations Control Conformational Switching of Inositol Pyrophosphate Analogues.
Resolution1.85 Å
Binding residue
(original residue number in PDB)
K53 K54 S102 K103 R213 K214 Y250 R262 S326 K329
Binding residue
(residue number reindexed from 1)
K12 K13 S61 K62 R172 K173 Y209 R221 S285 K288
Annotation score2
Enzymatic activity
Enzyme Commision number 2.7.4.24: diphosphoinositol-pentakisphosphate 1-kinase.
Gene Ontology
Molecular Function
GO:0000829 diphosphoinositol pentakisphosphate kinase activity

View graph for
Molecular Function
External links
PDB RCSB:5dgi, PDBe:5dgi, PDBj:5dgi
PDBsum5dgi
PubMed27460418
UniProtO43314|VIP2_HUMAN Inositol hexakisphosphate and diphosphoinositol-pentakisphosphate kinase 2 (Gene Name=PPIP5K2)

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