Structure of PDB 5dgh Chain A Binding Site BS02

Receptor Information
>5dgh Chain A (length=317) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
QIVVGICSMAKKSKSKPMKEILERISLFKYITVVVFEEEVILNEPVENWP
LCDCLISFHSKGFPLDKAVAYAKLRNPFVINDLNMQYLIQDRREVYSILQ
AEGILLPRYAILNRDPNNPKECNLIEGEDHVEVNGEVFQKPFVEKPVSAE
DHNVYIYYPTSAGGGSQRLFRKIGSRSSVYSPESNVRKTGSYIYEEFMPT
DGTDVKVYTVGPDYAHAEARKSPALDGKVERDSEGKEVRYPVILNAREKL
IAWKVCLAFKQTVCGFDLLRANGQSYVCDVNGFSFVKNSMKYYDDCAKIL
GNIVMRELAPQFHIPWS
Ligand information
Ligand ID5A3
InChIInChI=1S/C7H21O26P7/c8-34(9,10)1-35(11,12)28-2-3(29-36(13,14)15)5(31-38(19,20)21)7(33-40(25,26)27)6(32-39(22,23)24)4(2)30-37(16,17)18/h2-7H,1H2,(H,11,12)(H2,8,9,10)(H2,13,14,15)(H2,16,17,18)(H2,19,20,21)(H2,22,23,24)(H2,25,26,27)/t2-,3-,4+,5+,6-,7+
InChIKeyIZNCMXVIYGYGJI-AQWRHFAGSA-N
SMILES
SoftwareSMILES
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)=O)[CH]1O[P](O)(O)=O
OpenEye OEToolkits 1.9.2C(P(=O)(O)O)P(=O)(O)OC1[C@@H]([C@H](C([C@H]([C@@H]1OP(=O)(O)O)OP(=O)(O)O)OP(=O)(O)O)OP(=O)(O)O)OP(=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)(O)O)OP(=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)=O)[C@H]1O[P](O)(O)=O
ACDLabs 12.01O=P(OC1C(C(C(C(OP(CP(O)(O)=O)(=O)O)C1OP(O)(O)=O)OP(O)(O)=O)OP(O)(O)=O)OP(O)(=O)O)(O)O
FormulaC7 H21 O26 P7
NameMethylenebisphosphonate inositol pentakisphosphate;
{[(R)-hydroxy{[(1s,2R,3S,4s,5R,6S)-2,3,4,5,6-pentakis(phosphonooxy)cyclohexyl]oxy}phosphoryl]methyl}phosphonic acid
ChEMBLCHEMBL4278532
DrugBank
ZINCZINC000584904789
PDB chain5dgh 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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PDB5dgh Cellular Cations Control Conformational Switching of Inositol Pyrophosphate Analogues.
Resolution2.1 Å
Binding residue
(original residue number in PDB)
K53 K54 R213 K214 Y250 R262 R273 S326 K329
Binding residue
(residue number reindexed from 1)
K11 K12 R171 K172 Y208 R220 R231 S284 K287
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:5dgh, PDBe:5dgh, PDBj:5dgh
PDBsum5dgh
PubMed27460418
UniProtO43314|VIP2_HUMAN Inositol hexakisphosphate and diphosphoinositol-pentakisphosphate kinase 2 (Gene Name=PPIP5K2)

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