Structure of PDB 3byo Chain A Binding Site BS01

Receptor Information
>3byo 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 IDAM9
InChIInChI=1S/C31H30N8O/c1-20-7-6-8-21(2)27(20)39-29(40)24-19-32-30(35-28(24)38-26-10-5-4-9-25(26)34-31(38)39)33-22-11-13-23(14-12-22)37-17-15-36(3)16-18-37/h4-14,19H,15-18H2,1-3H3,(H,32,33,35)
InChIKeyBHJJWVDKNXABFS-UHFFFAOYSA-N
SMILES
SoftwareSMILES
CACTVS 3.341CN1CCN(CC1)c2ccc(Nc3ncc4C(=O)N(c5nc6ccccc6n5c4n3)c7c(C)cccc7C)cc2
OpenEye OEToolkits 1.5.0Cc1cccc(c1N2c3nc4ccccc4n3-c5c(cnc(n5)Nc6ccc(cc6)N7CCN(CC7)C)C2=O)C
ACDLabs 10.04O=C3N(c1c(cccc1C)C)c6nc7ccccc7n6c2nc(ncc23)Nc4ccc(cc4)N5CCN(C)CC5
FormulaC31 H30 N8 O
Name6-(2,6-dimethylphenyl)-2-{[4-(4-methylpiperazin-1-yl)phenyl]amino}pyrimido[5',4':5,6]pyrimido[1,2-a]benzimidazol-5(6H)-one
ChEMBLCHEMBL410295
DrugBank
ZINCZINC000053214756
PDB chain3byo 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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PDB3byo 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)		L251 V259 A271 K273 E288 T316 Y318 M319 G322 L371
Binding residue
(residue number reindexed from 1)		L21 V29 A41 K43 E58 T86 Y88 M89 G92 L141
Annotation score1
Binding affinityMOAD: ic50=7nM
PDBbind-CN: -logKd/Ki=8.15,IC50=7nM
BindingDB: IC50=1600nM
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

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Molecular Function
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Biological Process
External links
PDB RCSB:3byo, PDBe:3byo, PDBj:3byo
PDBsum3byo
PubMed18278858
UniProtP06239|LCK_HUMAN Tyrosine-protein kinase Lck (Gene Name=LCK)

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