Structure of PDB 5vsd Chain B Binding Site BS06

Receptor Information
>5vsd Chain B (length=258) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
VERIVSRDIARGYERIPIPCVNAVDSEPCPSNYKYVSQNCVTSPMNIDRN
ITHLQYCVCIDDCSSSNCMCGQLSMRCWYDKDGRLLPEFNMAEPPLIFEC
NHACSCWRNCRNRVVQNGLRARLQLYRTRDMGWGVRSLQDIPPGTFVCEY
VGELISDSEADVREEDSYLFDLDGEVYCIDARFYGNVSRFINHHCEPNLV
PVRVFMAHQDLRFPRIAFFSTRLIEAGEQLGFDYGERFWDIKGKLFSCRC
GSPKCRHS
Ligand information
Ligand ID9HJ
InChIInChI=1S/C20H31N5O2/c1-6-9-25(3)20-22-16-13-18(27-5)17(26-4)12-15(16)19(23-20)21-14-7-10-24(2)11-8-14/h12-14H,6-11H2,1-5H3,(H,21,22,23)
InChIKeyRCWUUMJJJVFQSV-UHFFFAOYSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 2.0.6CCCN(C)c1nc2cc(c(cc2c(n1)NC3CCN(CC3)C)OC)OC
CACTVS 3.385CCCN(C)c1nc(NC2CCN(C)CC2)c3cc(OC)c(OC)cc3n1
ACDLabs 12.01c12nc(nc(c1cc(c(c2)OC)OC)NC3CCN(C)CC3)N(C)CCC
FormulaC20 H31 N5 O2
Name6,7-dimethoxy-N~2~-methyl-N~4~-(1-methylpiperidin-4-yl)-N~2~-propylquinazoline-2,4-diamine
ChEMBLCHEMBL4072211
DrugBank
ZINC
PDB chain5vsd Chain B Residue 3006 [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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PDB5vsd Structure-activity relationship studies of G9a-like protein (GLP) inhibitors.
Resolution1.85 Å
Binding residue
(original residue number in PDB)		A1165 D1171 L1174 D1176 R1245 F1246 I1249 K1250
Binding residue
(residue number reindexed from 1)		A160 D166 L169 D171 R237 F238 I241 K242
Annotation score1
Binding affinityMOAD: Kd=57nM
BindingDB: Kd=57nM,IC50=5.0nM
Enzymatic activity
Catalytic site (original residue number in PDB) Y1155 Y1242
Catalytic site (residue number reindexed from 1) Y150 Y234
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:5vsd, PDBe:5vsd, PDBj:5vsd
PDBsum5vsd
PubMed28662962
UniProtQ9H9B1|EHMT1_HUMAN Histone-lysine N-methyltransferase EHMT1 (Gene Name=EHMT1)

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