Structure of PDB 6nm4 Chain B Binding Site BS03

Receptor Information
>6nm4 Chain B (length=183) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
EPQDDDYLYCEMCQNFFIDSCAAHGPPTFVKDSAVDKGHPNRSALSLPPG
LRIGPSGIPQAGLGVWNEASDLPLGLHFGPYEGRITEDEEAANNGYSWLI
TKGRNCYEYVDGKDKSWANWMRYVNCARDDEEQNLVAFQYHRQIFYRTCR
VIRPGCELLVWYGDEYGQELGIKWGSKWKKELM
Ligand information
Ligand IDKS7
InChIInChI=1S/C25H32N6O3/c1-18-13-20(5-8-26-18)30-9-6-25(7-10-30)17-31(12-11-29(25)2)24-27-23(28-34-24)19-14-21(32-3)16-22(15-19)33-4/h5,8,13-16H,6-7,9-12,17H2,1-4H3
InChIKeyNZYTZRHHBAJPKN-UHFFFAOYSA-N
SMILES
SoftwareSMILES
ACDLabs 12.01COc1cc(cc(c1)OC)c5noc(N2CCN(C4(C2)CCN(c3cc(ncc3)C)CC4)C)n5
CACTVS 3.385COc1cc(OC)cc(c1)c2noc(n2)N3CCN(C)C4(CCN(CC4)c5ccnc(C)c5)C3
OpenEye OEToolkits 2.0.6Cc1cc(ccn1)N2CCC3(CC2)CN(CCN3C)c4nc(no4)c5cc(cc(c5)OC)OC
FormulaC25 H32 N6 O3
Name4-[3-(3,5-dimethoxyphenyl)-1,2,4-oxadiazol-5-yl]-1-methyl-9-(2-methylpyridin-4-yl)-1,4,9-triazaspiro[5.5]undecane
ChEMBLCHEMBL4791017
DrugBank
ZINC
PDB chain6nm4 Chain B Residue 403 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB6nm4 Discovery of a chemical probe for PRDM9.
Resolution2.58 Å
Binding residue
(original residue number in PDB)		G290 S292 W293 C321 A322 D324 W356
Binding residue
(residue number reindexed from 1)		G95 S97 W98 C126 A127 D129 W161
Annotation score1
Enzymatic activity
Enzyme Commision number 2.1.1.-
2.1.1.354: [histone H3]-lysine(4) N-trimethyltransferase.
2.1.1.355: [histone H3]-lysine(9) N-trimethyltransferase.
2.1.1.359: [histone H3]-lysine(36) N-trimethyltransferase.
2.1.1.361: [histone H4]-lysine(20) N-methyltransferase.
2.1.1.362: [histone H4]-N-methyl-L-lysine(20) N-methyltransferase.
Gene Ontology
Molecular Function
GO:0042054 histone methyltransferase activity

View graph for
Molecular Function
External links
PDB RCSB:6nm4, PDBe:6nm4, PDBj:6nm4
PDBsum6nm4
PubMed31848333
UniProtQ9NQV7|PRDM9_HUMAN Histone-lysine N-methyltransferase PRDM9 (Gene Name=PRDM9)

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