Structure of PDB 6mbp Chain A Binding Site BS01

Receptor Information
>6mbp Chain A (length=261) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
VERIVSRDIARGYERIPIPCVNAVDSEPCPSNYKYVSQNCVTSPMNIDRN
ITHLQYCVCIDDCSSSNCMCGQLSMRCWYDKDGRLLPEFNMAEPPLIFEC
NHACSCWRNCRNRVVQNGLRARLQLYRTRDMGWGVRSLQDIPPGTFVCEY
VGELISDSEADVREEDSYLFDLDNKDGEVYCIDARFYGNVSRFINHHCEP
NLVPVRVFMAHQDLRFPRIAFFSTRLIEAGEQLGFDYGERFWDIKGKLFS
CRCGSPKCRHS
Ligand information
Ligand IDJDG
InChIInChI=1S/C31H49N5O2/c1-23(2)36-17-12-25(13-18-36)33-31-26-20-29(37-3)30(38-19-9-16-35-14-7-8-15-35)21-27(26)34-28(22-32-31)24-10-5-4-6-11-24/h20-21,23-25H,4-19,22H2,1-3H3,(H,32,33)
InChIKeyCEYUGMZUIYBLTQ-UHFFFAOYSA-N
SMILES
SoftwareSMILES
CACTVS 3.385COc1cc2C(=NCC(=Nc2cc1OCCCN3CCCC3)C4CCCCC4)NC5CCN(CC5)C(C)C
ACDLabs 12.01C1N(CCC1)CCCOc5c(cc2c(N=C(CN=C2NC3CCN(CC3)C(C)C)C4CCCCC4)c5)OC
OpenEye OEToolkits 2.0.6CC(C)N1CCC(CC1)NC2=NCC(=Nc3c2cc(c(c3)OCCCN4CCCC4)OC)C5CCCCC5
FormulaC31 H49 N5 O2
Name2-cyclohexyl-7-methoxy-N-[1-(propan-2-yl)piperidin-4-yl]-8-[3-(pyrrolidin-1-yl)propoxy]-3H-1,4-benzodiazepin-5-amine
ChEMBLCHEMBL4454542
DrugBank
ZINC
PDB chain6mbp Chain A Residue 2001 [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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PDB6mbp Discovery of a Novel Chemotype of Histone Lysine Methyltransferase EHMT1/2 (GLP/G9a) Inhibitors: Rational Design, Synthesis, Biological Evaluation, and Co-crystal Structure.
Resolution1.947 Å
Binding residue
(original residue number in PDB)		Y1124 D1131 A1134 R1137 D1140 S1141 L1143 D1145 V1153 R1214 F1215
Binding residue
(residue number reindexed from 1)		Y150 D157 A160 R163 D166 S167 L169 D171 V179 R240 F241
Annotation score1
Binding affinityPDBbind-CN: -logKd/Ki=5.95,Kd=1.13uM
Enzymatic activity
Catalytic site (original residue number in PDB) Y1124 Y1211
Catalytic site (residue number reindexed from 1) Y150 Y237
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:6mbp, PDBe:6mbp, PDBj:6mbp
PDBsum6mbp
PubMed30753076
UniProtQ9H9B1|EHMT1_HUMAN Histone-lysine N-methyltransferase EHMT1 (Gene Name=EHMT1)

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