Structure of PDB 3bym Chain A Binding Site BS01

Receptor Information
>3bym Chain A (length=272) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
QKPWWEDEWEVPRETLKLVERLGAGQFGEVWMGYYNGHTKVAVKSLKQGS
MSPDAFLAEANLMKQLQHQRLVRLYAVVTQEPIYIITEYMENGSLVDFLK
TPSGIKLTINKLLDMAAQIAEGMAFIEERNYIHRDLRAANILVSDTLSCK
IADFGLARLIEDNEYTAREGAKFPIKWTAPEAINYGTFTIKSDVWSFGIL
LTEIVTHGRIPYPGMTNPEVIQNLERGYRMVRPDNCPEELYQLMRLCWKE
RPEDRPTFDYLRSVLEDFFTAT
Ligand information
Ligand IDAM0
InChIInChI=1S/C25H23N7O3/c1-33-20-13-17(14-21(34-2)22(20)35-3)28-23-26-15-27-24(31-23)32-19-12-8-7-11-18(19)30-25(32)29-16-9-5-4-6-10-16/h4-15H,1-3H3,(H,29,30)(H,26,27,28,31)
InChIKeyOYDJAYPDIUTXRU-UHFFFAOYSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.5.0COc1cc(cc(c1OC)OC)Nc2ncnc(n2)n3c4ccccc4nc3Nc5ccccc5
CACTVS 3.341COc1cc(Nc2ncnc(n2)n3c(Nc4ccccc4)nc5ccccc35)cc(OC)c1OC
ACDLabs 10.04O(c1cc(cc(OC)c1OC)Nc2ncnc(n2)n3c5ccccc5nc3Nc4ccccc4)C
FormulaC25 H23 N7 O3
NameN-phenyl-1-{4-[(3,4,5-trimethoxyphenyl)amino]-1,3,5-triazin-2-yl}-1H-benzimidazol-2-amine
ChEMBLCHEMBL271131
DrugBank
ZINCZINC000029136121
PDB chain3bym 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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PDB3bym Structure-based design of novel 2-amino-6-phenyl-pyrimido[5',4':5,6]pyrimido[1,2-a]benzimidazol-5(6H)-ones as potent and orally active inhibitors of lymphocyte specific kinase (Lck): synthesis, SAR, and in vivo anti-inflammatory activity.
Resolution2.0 Å
Binding residue
(original residue number in PDB)		V259 A271 E288 M292 Y318 M319 G322 L371
Binding residue
(residue number reindexed from 1)		V30 A42 E59 M63 Y89 M90 G93 L142
Annotation score1
Binding affinityMOAD: ic50=0.006uM
PDBbind-CN: -logKd/Ki=8.22,IC50=6nM
BindingDB: IC50=6nM
Enzymatic activity
Catalytic site (original residue number in PDB) D364 R366 A368 N369 D382 A400 F402
Catalytic site (residue number reindexed from 1) D135 R137 A139 N140 D153 A171 F173
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

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Molecular Function
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Biological Process
External links
PDB RCSB:3bym, PDBe:3bym, PDBj:3bym
PDBsum3bym
PubMed18278858
UniProtP06239|LCK_HUMAN Tyrosine-protein kinase Lck (Gene Name=LCK)

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