Structure of PDB 5ghv Chain A Binding Site BS01

Receptor Information
>5ghv Chain A (length=265) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
VYLDRKLLTLEDKELGSGNFGTVKKGYYQMKKVVKTVAVKILKNPALKDE
LLAEANVMQQLDNPYIVRMIGICEAESWMLVMEMAELGPLNKYLQQNRHV
KDKNIIELVHQVSMGMKYLEESNFVHRDLAARNVLLVTQHYAKISDFGLS
KALRADENYYKAKWPVKWYAPECINYYKFSSKSDVWSFGVLMWEAFSYGQ
KPYRGMKGSEVTAMLEKGERMGCPAGCPREMYDLMNLCWTYDVENRPGFA
AVELRLRNYYYDVVN
Ligand information
Ligand IDX5G
InChIInChI=1S/C27H36N6O2/c1-19-12-23(13-20(2)26(19)35-11-10-31-8-4-5-9-31)29-27-28-7-6-25(30-27)33-14-21(3)22(16-33)15-32-17-24(34)18-32/h6-7,12-14,16,24,34H,4-5,8-11,15,17-18H2,1-3H3,(H,28,29,30)
InChIKeyCXYOUSONGUCKEF-UHFFFAOYSA-N
SMILES
SoftwareSMILES
CACTVS 3.385Cc1cn(cc1CN2CC(O)C2)c3ccnc(Nc4cc(C)c(OCCN5CCCC5)c(C)c4)n3
ACDLabs 12.01O(c4c(cc(Nc3nc(n1cc(c(c1)CN2CC(O)C2)C)ccn3)cc4C)C)CCN5CCCC5
OpenEye OEToolkits 1.9.2Cc1cc(cc(c1OCCN2CCCC2)C)Nc3nccc(n3)n4cc(c(c4)CN5CC(C5)O)C
FormulaC27 H36 N6 O2
Name1-({1-[2-({3,5-dimethyl-4-[2-(pyrrolidin-1-yl)ethoxy]phenyl}amino)pyrimidin-4-yl]-4-methyl-1H-pyrrol-3-yl}methyl)azetidin-3-ol
ChEMBLCHEMBL3622942
DrugBank
ZINCZINC000263620338
PDB chain5ghv Chain A Residue 701 [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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PDB5ghv Crystal structures of spleen tyrosine kinase in complex with novel inhibitors: structural insights for design of anticancer drugs
Resolution2.8 Å
Binding residue
(original residue number in PDB)		L377 A400 M448 M450 A451 G454 P455 R498 L501 D512
Binding residue
(residue number reindexed from 1)		L15 A38 M82 M84 A85 G88 P89 R132 L135 D146
Annotation score1
Binding affinityPDBbind-CN: -logKd/Ki=7.92,IC50=12.1nM
BindingDB: IC50=12nM
Enzymatic activity
Catalytic site (original residue number in PDB) D494 A496 R498 N499 D512 K533
Catalytic site (residue number reindexed from 1) D128 A130 R132 N133 D146 K163
Enzyme Commision number 2.7.10.2: non-specific protein-tyrosine kinase.
Gene Ontology
Molecular Function
GO:0004672 protein kinase activity
GO:0004713 protein tyrosine kinase activity
GO:0005524 ATP binding
Biological Process
GO:0006468 protein phosphorylation

View graph for
Molecular Function
View graph for
Biological Process
External links
PDB RCSB:5ghv, PDBe:5ghv, PDBj:5ghv
PDBsum5ghv
PubMed27504936
UniProtP43405|KSYK_HUMAN Tyrosine-protein kinase SYK (Gene Name=SYK)

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