Structure of PDB 3mo0 Chain A Binding Site BS02

Receptor Information
>3mo0 Chain A (length=251) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
RIVSRDIARGYERIPIPCVNAVDSEPCPSNYKYVSQNCVTSITHLQYCVC
IDDCSSSNCMCGQLSMRCWYDKDGRLLPEFNMAEPPLIFECNHACSCWRN
CRNRVVQNGLRARLQLYRTRDMGWGVRSLQDIPPGTFVCEYVGELISDSE
ADVREEDSYLFDLDNKDGEVYCIDARFYGNVSRFINHHCEPNLVPVRVFM
AHQDLRFPRIAFFSTRLIEAGEQLGFDYGERFWDIKGKLFSCRCGSPKCR
H
Ligand information
Ligand IDE11
InChIInChI=1S/C27H38N6O2/c1-32(2)14-8-13-28-27-30-23-18-25(35-4)24(34-3)17-22(23)26(31-27)29-21-11-15-33(16-12-21)19-20-9-6-5-7-10-20/h5-7,9-10,17-18,21H,8,11-16,19H2,1-4H3,(H2,28,29,30,31)
InChIKeyYYFDMPHIONBOKZ-UHFFFAOYSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.7.0CN(C)CCCNc1nc2cc(c(cc2c(n1)NC3CCN(CC3)Cc4ccccc4)OC)OC
ACDLabs 12.01O(c4cc1c(nc(nc1NC3CCN(Cc2ccccc2)CC3)NCCCN(C)C)cc4OC)C
CACTVS 3.370COc1cc2nc(NCCCN(C)C)nc(NC3CCN(CC3)Cc4ccccc4)c2cc1OC
FormulaC27 H38 N6 O2
NameN~4~-(1-benzylpiperidin-4-yl)-N~2~-[3-(dimethylamino)propyl]-6,7-dimethoxyquinazoline-2,4-diamine
ChEMBLCHEMBL1232432
DrugBank
ZINCZINC000058631426
PDB chain3mo0 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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PDB3mo0 Adding a lysine mimic in the design of potent inhibitors of histone lysine methyltransferases.
Resolution2.78 Å
Binding residue
(original residue number in PDB)		D1131 A1134 D1135 E1138 D1140 L1143 D1145 R1214 F1215 K1219
Binding residue
(residue number reindexed from 1)		D148 A151 D152 E155 D157 L160 D162 R231 F232 K236
Annotation score1
Binding affinityPDBbind-CN: -logKd/Ki=6.81,Kd=154nM
Enzymatic activity
Catalytic site (original residue number in PDB) Y1124 Y1211
Catalytic site (residue number reindexed from 1) Y141 Y228
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
GO:0046974 histone H3K9 methyltransferase activity
Cellular Component
GO:0005634 nucleus

View graph for
Molecular Function
View graph for
Cellular Component
External links
PDB RCSB:3mo0, PDBe:3mo0, PDBj:3mo0
PDBsum3mo0
PubMed20434463
UniProtQ9H9B1|EHMT1_HUMAN Histone-lysine N-methyltransferase EHMT1 (Gene Name=EHMT1)

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