Structure of PDB 6n5c Chain A Binding Site BS05

Receptor Information
>6n5c 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 IDKDJ
InChIInChI=1S/C8H19F2NO24P6/c9-8(10,36(13,14)15)7(12)11-1-2(31-37(16,17)18)4(33-39(22,23)24)6(35-41(28,29)30)5(34-40(25,26)27)3(1)32-38(19,20)21/h1-6H,(H,11,12)(H2,13,14,15)(H2,16,17,18)(H2,19,20,21)(H2,22,23,24)(H2,25,26,27)(H2,28,29,30)/t1-,2-,3+,4+,5-,6+
InChIKeyXBHZOGSBYRIXJA-QWBQGLJISA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 2.0.6C1(C(C(C(C(C1OP(=O)(O)O)OP(=O)(O)O)OP(=O)(O)O)OP(=O)(O)O)OP(=O)(O)O)NC(=O)C(F)(F)P(=O)(O)O
CACTVS 3.385O[P](O)(=O)O[C@H]1[C@H](NC(=O)C(F)(F)[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
OpenEye OEToolkits 2.0.6[C@H]1([C@H](C([C@H]([C@@H](C1NC(=O)C(F)(F)P(=O)(O)O)OP(=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)O[CH]1[CH](NC(=O)C(F)(F)[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
ACDLabs 12.01N(C(C(P(O)(O)=O)(F)F)=O)C1C(C(C(C(C1OP(O)(O)=O)OP(O)(O)=O)OP(O)(=O)O)OP(O)(=O)O)OP(O)(O)=O
FormulaC8 H19 F2 N O24 P6
Name(1,1-difluoro-2-oxo-2-{[(1s,2R,3S,4s,5R,6S)-2,3,4,5,6-pentakis(phosphonooxy)cyclohexyl]amino}ethyl)phosphonic acid
ChEMBLCHEMBL4595084
DrugBank
ZINC
PDB chain6n5c Chain A Residue 406 [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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PDB6n5c Synthesis of an alpha-phosphono-alpha , alpha-difluoroacetamide analogue of the diphosphoinositol pentakisphosphate 5-InsP7.
Resolution1.95 Å
Binding residue
(original residue number in PDB)		K53 K54 R213 K214 K248 R262 S326 K329
Binding residue
(residue number reindexed from 1)		K11 K12 R171 K172 K206 R220 S284 K287
Annotation score2
Binding affinityPDBbind-CN: -logKd/Ki=6.43,IC50=375nM
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:6n5c, PDBe:6n5c, PDBj:6n5c
PDBsum6n5c
PubMed31391889
UniProtO43314|VIP2_HUMAN Inositol hexakisphosphate and diphosphoinositol-pentakisphosphate kinase 2 (Gene Name=PPIP5K2)

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