Structure of PDB 6nm4 Chain B Binding Site BS02

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 IDSAM
InChIInChI=1S/C15H22N6O5S/c1-27(3-2-7(16)15(24)25)4-8-10(22)11(23)14(26-8)21-6-20-9-12(17)18-5-19-13(9)21/h5-8,10-11,14,22-23H,2-4,16H2,1H3,(H2-,17,18,19,24,25)/t7-,8+,10+,11+,14+,27-/m0/s1
InChIKeyMEFKEPWMEQBLKI-FCKMPRQPSA-N
SMILES
SoftwareSMILES
CACTVS 3.341C[S@@+](CC[C@H](N)C([O-])=O)C[C@H]1O[C@H]([C@H](O)[C@@H]1O)n2cnc3c(N)ncnc23
OpenEye OEToolkits 1.5.0C[S+](CCC(C(=O)[O-])N)CC1C(C(C(O1)n2cnc3c2ncnc3N)O)O
CACTVS 3.341C[S+](CC[CH](N)C([O-])=O)C[CH]1O[CH]([CH](O)[CH]1O)n2cnc3c(N)ncnc23
OpenEye OEToolkits 1.5.0C[S@@+](CC[C@@H](C(=O)[O-])N)C[C@@H]1[C@H]([C@H]([C@@H](O1)n2cnc3c2ncnc3N)O)O
ACDLabs 10.04[O-]C(=O)C(N)CC[S+](C)CC3OC(n2cnc1c(ncnc12)N)C(O)C3O
FormulaC15 H22 N6 O5 S
NameS-ADENOSYLMETHIONINE
ChEMBLCHEMBL1235831
DrugBank
ZINC
PDB chain6nm4 Chain B Residue 402 [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)		A256 G257 L258 G290 Y291 R317 Y318 N320 C321
Binding residue
(residue number reindexed from 1)		A61 G62 L63 G95 Y96 R122 Y123 N125 C126
Annotation score5
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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