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Structure of PDB 3fpd Chain B Binding Site BS02

Receptor Information
>3fpd Chain B (length=260) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
ERIVSRDIARGYERIPIPCVNAVDSEPCPSNYKYVSQNCVTSPMNIDRNI
THLQYCVCIDDCSSSNCMCGQLSMRCWYDKDGRLLPEFNMAEPPLIFECN
HACSCWRNCRNRVVQNGLRARLQLYRTRDMGWGVRSLQDIPPGTFVCEYV
GELISDSEADVREEDSYLFDLDNKDGEVYCIDARFYGNVSRFINHHCEPN
LVPVRVFMAHQDLRFPRIAFFSTRLIEAGEQLGFDYGERFWDIKGKLFSC
RCGSPKCRHS
Ligand information
Ligand IDQ4A
InChIInChI=1S/C28H38N6O2/c1-32-12-7-13-34(17-16-32)28-30-24-19-26(36-3)25(35-2)18-23(24)27(31-28)29-22-10-14-33(15-11-22)20-21-8-5-4-6-9-21/h4-6,8-9,18-19,22H,7,10-17,20H2,1-3H3,(H,29,30,31)
InChIKeyOSXFATOLZGZLSK-UHFFFAOYSA-N
SMILES
SoftwareSMILES
CACTVS 3.341COc1cc2nc(nc(NC3CCN(CC3)Cc4ccccc4)c2cc1OC)N5CCCN(C)CC5
OpenEye OEToolkits 1.5.0C[N@@]1CCCN(CC1)c2nc3cc(c(cc3c(n2)NC4CCN(CC4)Cc5ccccc5)OC)OC
ACDLabs 10.04O(c5cc1c(nc(nc1NC3CCN(Cc2ccccc2)CC3)N4CCCN(C)CC4)cc5OC)C
OpenEye OEToolkits 1.5.0CN1CCCN(CC1)c2nc3cc(c(cc3c(n2)NC4CCN(CC4)Cc5ccccc5)OC)OC
FormulaC28 H38 N6 O2
NameN-(1-benzylpiperidin-4-yl)-6,7-dimethoxy-2-(4-methyl-1,4-diazepan-1-yl)quinazolin-4-amine
ChEMBLCHEMBL569864
DrugBank
ZINCZINC000036382102
PDB chain3fpd Chain B Residue 2 [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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PDB3fpd Structural basis for G9a-like protein lysine methyltransferase inhibition by BIX-01294.
Resolution2.4 Å
Binding residue
(original residue number in PDB)		D1131 A1134 D1135 V1136 E1138 D1140 L1143 D1145 R1214 F1215
Binding residue
(residue number reindexed from 1)		D156 A159 D160 V161 E163 D165 L168 D170 R239 F240
Annotation score1
Binding affinityMOAD: ic50=0.7uM
BindingDB: IC50=700nM
Enzymatic activity
Catalytic site (original residue number in PDB) Y1124 Y1211
Catalytic site (residue number reindexed from 1) Y149 Y236
Enzyme Commision number 2.1.1.-
2.1.1.367: [histone H3]-lysine(9) N-methyltransferase.
Gene Ontology
Molecular Function
GO:0002039 p53 binding
GO:0008270 zinc ion binding
GO:0016279 protein-lysine N-methyltransferase activity
GO:0042054 histone methyltransferase activity
Cellular Component
GO:0005634 nucleus

View graph for
Molecular Function
View graph for
Cellular Component
External links
PDB RCSB:3fpd, PDBe:3fpd, PDBj:3fpd
PDBsum3fpd
PubMed19219047
UniProtQ9H9B1|EHMT1_HUMAN Histone-lysine N-methyltransferase EHMT1 (Gene Name=EHMT1)

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