Structure of PDB 6mbo Chain A Binding Site BS01

Receptor Information
>6mbo 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 chain6mbo Chain A Residue 1301 [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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PDB6mbo Discovery of a Novel Chemotype of Histone Lysine Methyltransferase EHMT1/2 (GLP/G9a) Inhibitors: Rational Design, Synthesis, Biological Evaluation, and Co-crystal Structure.
Resolution1.591 Å
Binding residue
(original residue number in PDB)		T1026 Y1030
Binding residue
(residue number reindexed from 1)		T52 Y56
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:6mbo, PDBe:6mbo, PDBj:6mbo
PDBsum6mbo
PubMed30753076
UniProtQ9H9B1|EHMT1_HUMAN Histone-lysine N-methyltransferase EHMT1 (Gene Name=EHMT1)

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