Structure of PDB 3byu Chain A Binding Site BS01

Receptor Information
>3byu Chain A (length=256) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
KPWWEDEWEVPRETLKLVERLGAGQFGEVWMGYYNGHTKVAVKSLKQGSM
SPDAFLAEANLMKQLQHQRLVRLYAVVTQEPIYIITEYMENGSLVDFLKT
PSGIKLTINKLLDMAAQIAEGMAFIEERNYIHRDLRAANILVSDTLSCKI
ADFGLKFPIKWTAPEAINYGTFTIKSDVWSFGILLTEIVTHGRIPYPGMT
NPEVIQNLERGYRMVRPDNCPEELYQLMRLCWKERPEDRPTFDYLRSVLE
DFFTAT
Ligand information
Ligand IDAM6
InChIInChI=1S/C32H32F3N7O2/c1-20-7-8-23(38-29(43)26-5-4-6-28(21(26)2)32(33,34)35)17-27(20)30(44)39-24-18-36-31(37-19-24)40-22-9-11-25(12-10-22)42-15-13-41(3)14-16-42/h4-12,17-19H,13-16H2,1-3H3,(H,38,43)(H,39,44)(H,36,37,40)
InChIKeyYNJXLRWECIJSPA-UHFFFAOYSA-N
SMILES
SoftwareSMILES
CACTVS 3.341CN1CCN(CC1)c2ccc(Nc3ncc(NC(=O)c4cc(NC(=O)c5cccc(c5C)C(F)(F)F)ccc4C)cn3)cc2
OpenEye OEToolkits 1.5.0Cc1ccc(cc1C(=O)Nc2cnc(nc2)Nc3ccc(cc3)N4CCN(CC4)C)NC(=O)c5cccc(c5C)C(F)(F)F
ACDLabs 10.04FC(F)(F)c1cccc(c1C)C(=O)Nc2cc(c(cc2)C)C(=O)Nc3cnc(nc3)Nc4ccc(cc4)N5CCN(C)CC5
FormulaC32 H32 F3 N7 O2
Name2-methyl-N-{4-methyl-3-[(2-{[4-(4-methylpiperazin-1-yl)phenyl]amino}pyrimidin-5-yl)carbamoyl]phenyl}-3-(trifluoromethyl)benzamide
ChEMBLCHEMBL271140
DrugBank
ZINCZINC000053059129
PDB chain3byu Chain A Residue 1 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB3byu Structure-guided design of aminopyrimidine amides as potent, selective inhibitors of lymphocyte specific kinase: synthesis, structure-activity relationships, and inhibition of in vivo T cell activation.
Resolution2.3 Å
Binding residue
(original residue number in PDB)		A271 V272 K273 E288 M292 T316 Y318 M319 G322 L371 A381 D382 F383
Binding residue
(residue number reindexed from 1)		A41 V42 K43 E58 M62 T86 Y88 M89 G92 L141 A151 D152 F153
Annotation score1
Binding affinityMOAD: ic50=0.8nM
PDBbind-CN: -logKd/Ki=9.10,IC50=0.8nM
BindingDB: IC50=0.8nM
Enzymatic activity
Catalytic site (original residue number in PDB) D364 R366 A368 N369 D382 F402
Catalytic site (residue number reindexed from 1) D134 R136 A138 N139 D152 F157
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
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Biological Process
External links
PDB RCSB:3byu, PDBe:3byu, PDBj:3byu
PDBsum3byu
PubMed18321037
UniProtP06239|LCK_HUMAN Tyrosine-protein kinase Lck (Gene Name=LCK)

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