Structure of PDB 3mo0 Chain B Binding Site BS01

Receptor Information
>3mo0 Chain B (length=242) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
IVSRDIARGYERIPIPCVNAVDSEPCPSNYKYVSQNCVTSPMNIDRNITH
LQYCVCIDDCSSSNCMCGQLSMRCPPLIFECNHACSCWRNCRNRVVQNGL
RARLQLYRTRDMGWGVRSLQDIPPGTFVCEYVGELISDSEADVREEDSYL
FDLDNKDGEVYCIDARFYGNVSRFINHHCEPNLVPVRVFMAHQDLRFPRI
AFFSTRLIEAGEQLGFDYGERFWDIKGKLFSCRCGSPKCRHS
Ligand information
Ligand IDSAH
InChIInChI=1S/C14H20N6O5S/c15-6(14(23)24)1-2-26-3-7-9(21)10(22)13(25-7)20-5-19-8-11(16)17-4-18-12(8)20/h4-7,9-10,13,21-22H,1-3,15H2,(H,23,24)(H2,16,17,18)/t6-,7+,9+,10+,13+/m0/s1
InChIKeyZJUKTBDSGOFHSH-WFMPWKQPSA-N
SMILES
SoftwareSMILES
CACTVS 3.341N[CH](CCSC[CH]1O[CH]([CH](O)[CH]1O)n2cnc3c(N)ncnc23)C(O)=O
OpenEye OEToolkits 1.5.0c1nc(c2c(n1)n(cn2)C3C(C(C(O3)CSCCC(C(=O)O)N)O)O)N
CACTVS 3.341N[C@@H](CCSC[C@H]1O[C@H]([C@H](O)[C@@H]1O)n2cnc3c(N)ncnc23)C(O)=O
ACDLabs 10.04O=C(O)C(N)CCSCC3OC(n2cnc1c(ncnc12)N)C(O)C3O
OpenEye OEToolkits 1.5.0c1nc(c2c(n1)n(cn2)[C@H]3[C@@H]([C@@H]([C@H](O3)CSCC[C@@H](C(=O)O)N)O)O)N
FormulaC14 H20 N6 O5 S
NameS-ADENOSYL-L-HOMOCYSTEINE
ChEMBLCHEMBL418052
DrugBankDB01752
ZINCZINC000004228232
PDB chain3mo0 Chain B Residue 102 [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)		M1105 W1107 S1141 Y1142 R1166 N1169 H1170 Y1211 F1223 C1225 R1226
Binding residue
(residue number reindexed from 1)		M112 W114 S148 Y149 R173 N176 H177 Y218 F230 C232 R233
Annotation score5
Binding affinityBindingDB: IC50=230nM
Enzymatic activity
Catalytic site (original residue number in PDB) Y1124 Y1211
Catalytic site (residue number reindexed from 1) Y131 Y218
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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