Structure of PDB 6nm4 Chain A Binding Site BS03

Receptor Information
>6nm4 Chain A (length=185) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
SEPQDDDYLYCEMCQNFFIDSCAAHGPPTFVKDSAVDKGHPNRSALSLPP
GLRIGPSGIPQAGLGVWNEASDLPLGLHFGPYEGRITEDEEAANNGYSWL
ITKGRNCYEYVDGKDKSWANWMRYVNCARDDEEQNLVAFQYHRQIFYRTC
RVIRPGCELLVWYGDEYGQELGIKWGSKWKKELMA
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 A Residue 403 [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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PDB6nm4 Discovery of a chemical probe for PRDM9.
Resolution2.58 Å
Binding residue
(original residue number in PDB)		W293 C321 A322 D324 W356
Binding residue
(residue number reindexed from 1)		W99 C127 A128 D130 W162
Annotation score1
Binding affinityPDBbind-CN: -logKd/Ki=7.06,Kd=87nM
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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