Structure of PDB 3kmm Chain A Binding Site BS01

Receptor Information
>3kmm Chain A (length=271) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
KPWWEDEWEVPRETLKLVERLGAGQFGEVWMGYYNGHTKVAVKSLKQGSM
SPDAFLAEANLMKQLQHQRLVRLYAVVTQEPIYIITEYMENGSLVDFLKT
PSGIKLTINKLLDMAAQIAEGMAFIEERNYIHRDLRAANILVSDTLSCKI
ADFGLARLIEDNEYTAREGAKFPIKWTAPEAINYGTFTIKSDVWSFGILL
TEIVTHGRIPYPGMTNPEVIQNLERGYRMVRPDNCPEELYQLMRLCWKER
PEDRPTFDYLRSVLEDFFTAT
Ligand information
Ligand IDLHL
InChIInChI=1S/C25H28Cl2N6O2/c1-4-32(5-2)13-14-35-19-11-9-18(10-12-19)29-24-28-15-17-16-33(25(34)31(3)23(17)30-24)22-20(26)7-6-8-21(22)27/h6-12,15H,4-5,13-14,16H2,1-3H3,(H,28,29,30)
InChIKeyLQYPBKQMDVWUGO-UHFFFAOYSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.7.0CCN(CC)CCOc1ccc(cc1)Nc2ncc3c(n2)N(C(=O)N(C3)c4c(cccc4Cl)Cl)C
CACTVS 3.352CCN(CC)CCOc1ccc(Nc2ncc3CN(C(=O)N(C)c3n2)c4c(Cl)cccc4Cl)cc1
FormulaC25 H28 Cl2 N6 O2
Name3-(2,6-dichlorophenyl)-7-({4-[2-(diethylamino)ethoxy]phenyl}amino)-1-methyl-3,4-dihydropyrimido[4,5-d]pyrimidin-2(1H)-one
ChEMBLCHEMBL1234002
DrugBank
ZINCZINC000058639016
PDB chain3kmm 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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PDB3kmm Structural Basis for Activation of Human Lymphocyte Kinase Lck Upon Tyrosine Phosphorylation
Resolution2.8 Å
Binding residue
(original residue number in PDB)		V259 A271 V272 K273 E288 T316 Y318 M319 G322 L371 D382
Binding residue
(residue number reindexed from 1)		V29 A41 V42 K43 E58 T86 Y88 M89 G92 L141 D152
Annotation score1
Binding affinityPDBbind-CN: -logKd/Ki=9.70,Kd=0.2nM
BindingDB: Kd=0.2nM
Enzymatic activity
Catalytic site (original residue number in PDB) D364 R366 A368 N369 D382 A400 F402
Catalytic site (residue number reindexed from 1) D134 R136 A138 N139 D152 A170 F172
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:3kmm, PDBe:3kmm, PDBj:3kmm
PDBsum3kmm
PubMed
UniProtP06239|LCK_HUMAN Tyrosine-protein kinase Lck (Gene Name=LCK)

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