Structure of PDB 3k5k Chain A Binding Site BS06

Receptor Information
>3k5k 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]
RTEKIICRDVARGYENVPIPCVNGVDGEPCPEDYKYISENCETSTMNIDR
NITHLQHCTCVDDCSSSNCLCGQLSIRCWYDKDGRLLQEFNKIEPPLIFE
CNQACSCWRNCKNRVVQSGIKVRLQLYRTAKMGWGVRALQTIPQGTFICE
YVGELISDAEADVREDDSYLFDLDNKEVYCIDARYYGNISRFINHLCDPN
IIPVRVFMLHQDLRFPRIAFFSSRDIRTGEELGFDYGDRFWDIKSKYFTC
QCGSEKCKHSAEAIALEQSRLA
Ligand information
Ligand IDDXQ
InChIInChI=1S/C26H43N7O2/c1-30(2)10-7-17-35-24-19-22-21(18-23(24)34-5)25(27-20-8-13-32(4)14-9-20)29-26(28-22)33-12-6-11-31(3)15-16-33/h18-20H,6-17H2,1-5H3,(H,27,28,29)
InChIKeyXIVUGRBSBIXXJE-UHFFFAOYSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.7.0C[N@]1CCCN(CC1)c2nc3cc(c(cc3c(n2)NC4CCN(CC4)C)OC)OCCCN(C)C
CACTVS 3.352COc1cc2c(NC3CCN(C)CC3)nc(nc2cc1OCCCN(C)C)N4CCCN(C)CC4
OpenEye OEToolkits 1.7.0CN1CCCN(CC1)c2nc3cc(c(cc3c(n2)NC4CCN(CC4)C)OC)OCCCN(C)C
ACDLabs 11.02O(c3cc2nc(nc(NC1CCN(C)CC1)c2cc3OC)N4CCCN(C)CC4)CCCN(C)C
FormulaC26 H43 N7 O2
Name7-[3-(dimethylamino)propoxy]-6-methoxy-2-(4-methyl-1,4-diazepan-1-yl)-N-(1-methylpiperidin-4-yl)quinazolin-4-amine
ChEMBLCHEMBL576781
DrugBank
ZINCZINC000036382580
PDB chain3k5k Chain A Residue 2000 [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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PDB3k5k Discovery of a 2,4-diamino-7-aminoalkoxyquinazoline as a potent and selective inhibitor of histone lysine methyltransferase G9a.
Resolution1.7 Å
Binding residue
(original residue number in PDB)		D1074 A1077 D1078 D1083 L1086 D1088 F1152 Y1154 R1157 F1158
Binding residue
(residue number reindexed from 1)		D158 A161 D162 D167 L170 D172 F234 Y236 R239 F240
Annotation score1
Binding affinityMOAD: Kd=23nM
PDBbind-CN: -logKd/Ki=7.64,Kd=23nM
BindingDB: IC50=15nM,Ki=2.6nM,Kd=23nM
Enzymatic activity
Catalytic site (original residue number in PDB) Y1067 Y1154
Catalytic site (residue number reindexed from 1) Y151 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:3k5k, PDBe:3k5k, PDBj:3k5k
PDBsum3k5k
PubMed19891491
UniProtQ96KQ7|EHMT2_HUMAN Histone-lysine N-methyltransferase EHMT2 (Gene Name=EHMT2)

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