Structure of PDB 7xub Chain A Binding Site BS06

Receptor Information
>7xub Chain A (length=270) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
IRTEKIICRDVARGYENVPIPCVNGVDGEPCPEDYKYISENCETSTMNID
RNITHLQHCTCVDDCSSSNCLCGQLSIRCWYDKDGRLLQEFNKIEPPLIF
ECNQACSCWRNCKNRVVQSGIKVRLQLYRTAKMGWGVRALQTIPQGTFIC
EYVGELISDAEADVREDDSYLFDLDNKDGEVYCIDARYYGNISRFINHLC
DPNIIPVRVFMLHQDLRFPRIAFFSSRDIRTGEELGFDYGDRFWDIKSKY
FTCQCGSEKCKHSAEAIALE
Ligand information
Ligand IDI6L
InChIInChI=1S/C24H30N4O2/c1-5-6-9-17(22-26-15-10-7-8-11-16(15)27-22)28-23(30)21-14(2)20-18(25-21)12-24(3,4)13-19(20)29/h7-8,10-11,17,25H,5-6,9,12-13H2,1-4H3,(H,26,27)(H,28,30)/t17-/m0/s1
InChIKeyMLILCMJFXVXZFP-KRWDZBQOSA-N
SMILES
SoftwareSMILES
CACTVS 3.385CCCC[CH](NC(=O)c1[nH]c2CC(C)(C)CC(=O)c2c1C)c3[nH]c4ccccc4n3
CACTVS 3.385CCCC[C@H](NC(=O)c1[nH]c2CC(C)(C)CC(=O)c2c1C)c3[nH]c4ccccc4n3
OpenEye OEToolkits 2.0.7CCCCC(c1[nH]c2ccccc2n1)NC(=O)c3c(c4c([nH]3)CC(CC4=O)(C)C)C
OpenEye OEToolkits 2.0.7CCCC[C@@H](c1[nH]c2ccccc2n1)NC(=O)c3c(c4c([nH]3)CC(CC4=O)(C)C)C
FormulaC24 H30 N4 O2
Name~{N}-[(1~{S})-1-(1~{H}-benzimidazol-2-yl)pentyl]-3,6,6-trimethyl-4-oxidanylidene-5,7-dihydro-1~{H}-indole-2-carboxamide
ChEMBLCHEMBL5284990
DrugBank
ZINC
PDB chain7xub Chain A Residue 1206 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB7xub Discovery of Novel Substrate-Competitive Lysine Methyltransferase G9a Inhibitors as Anticancer Agents.
Resolution2.0 Å
Binding residue
(original residue number in PDB)		D1083 S1084 L1086 F1087 D1088 P1121 F1152 Y1154 R1157 F1158
Binding residue
(residue number reindexed from 1)		D168 S169 L171 F172 D173 P206 F237 Y239 R242 F243
Annotation score1
Enzymatic activity
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:7xub, PDBe:7xub, PDBj:7xub
PDBsum7xub
PubMed36882960
UniProtQ96KQ7|EHMT2_HUMAN Histone-lysine N-methyltransferase EHMT2 (Gene Name=EHMT2)

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