Structure of PDB 4yhf Chain A Binding Site BS01

Receptor Information
>4yhf Chain A (length=268) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
GYGSWEIDPKDLTFLKELGTGQFGVVKYGKWRGQYDVAIKMIKEGSMSED
EFIEEAKVMMNLSHEKLVQLYGVCTKQRPIFIITEYMANGCLLNYLREMR
HRFQTQQLLEMCKDVCEAMEYLESKQFLHRDLAARNCLVNDQGVVKVSDF
GLSRYVLDDEYTSSVGSKFPVRWSPPEVLMYSKFSSKSDIWAFGVLMWEI
YSLGKMPYERFTNSETAEHIAQGLRLYRPHLASEKVYTIMYSCWHEKADE
RPTFKILLSNILDVMDEE
Ligand information
Ligand ID4C9
InChIInChI=1S/C30H33N7O2/c1-30(2,3)16-21(17-31)29(38)36-15-7-8-22(18-36)37-28-25(27(32)33-19-34-28)26(35-37)20-11-13-24(14-12-20)39-23-9-5-4-6-10-23/h4-6,9-14,19,21-22H,7-8,15-16,18H2,1-3H3,(H2,32,33,34)/t21-,22-/m1/s1
InChIKeyDZSBLWYJPNCWLI-FGZHOGPDSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.7.6CC(C)(C)CC(C#N)C(=O)N1CCC[C@H](C1)n2c3c(c(n2)c4ccc(cc4)Oc5ccccc5)c(ncn3)N
CACTVS 3.385CC(C)(C)C[C@@H](C#N)C(=O)N1CCC[C@H](C1)n2nc(c3ccc(Oc4ccccc4)cc3)c5c(N)ncnc25
OpenEye OEToolkits 1.7.6CC(C)(C)CC(C#N)C(=O)N1CCCC(C1)n2c3c(c(n2)c4ccc(cc4)Oc5ccccc5)c(ncn3)N
CACTVS 3.385CC(C)(C)C[CH](C#N)C(=O)N1CCC[CH](C1)n2nc(c3ccc(Oc4ccccc4)cc3)c5c(N)ncnc25
ACDLabs 12.01N#CC(C(=O)N5CCCC(n2nc(c1c(ncnc12)N)c4ccc(Oc3ccccc3)cc4)C5)CC(C)(C)C
FormulaC30 H33 N7 O2
Name(2S)-2-({(3R)-3-[4-amino-3-(4-phenoxyphenyl)-1H-pyrazolo[3,4-d]pyrimidin-1-yl]piperidin-1-yl}carbonyl)-4,4-dimethylpentanenitrile
ChEMBL
DrugBank
ZINCZINC000263620391
PDB chain4yhf 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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PDB4yhf Prolonged and tunable residence time using reversible covalent kinase inhibitors.
Resolution2.2 Å
Binding residue
(original residue number in PDB)		V416 A428 K430 M449 V458 I472 T474 Y476 M477 G480 C481 N484 S538 D539 F540 L542
Binding residue
(residue number reindexed from 1)		V26 A38 K40 M59 V68 I82 T84 Y86 M87 G90 C91 N94 S148 D149 F150 L152
Annotation score1
Binding affinityPDBbind-CN: -logKd/Ki=8.34,IC50=4.6nM
Enzymatic activity
Catalytic site (original residue number in PDB) D521 A523 R525 N526 D539 F559
Catalytic site (residue number reindexed from 1) D131 A133 R135 N136 D149 F169
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:4yhf, PDBe:4yhf, PDBj:4yhf
PDBsum4yhf
PubMed26006010
UniProtQ06187|BTK_HUMAN Tyrosine-protein kinase BTK (Gene Name=BTK)

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