Structure of PDB 7yrg Chain L Binding Site BS04

Receptor Information

>7yrg Chain L (length=240) Species: 9606 (Homo sapiens)

GQSRYVPSSGMSAKELCENDDLATSLVLDPYLGFQTHKMNTRQELKEVIE
RFKKDEHLEKNKMQEKLFKEHVFIYLRMFATDSGFEILPCNRYSSEQNGA
KIVATKEWKRNDKIELLVGCIAELSEIEENMLLRHGENDFSVMYSTRKNC
AQLWLGPAAFINHDCRPNCKFVSTGRDTACVKALRDIEPGEEISCYYGDG
FFGENNEFCECYTCERRGTGAFKSKYGLRETDKRLNRLKK

Ligand information

• Ligand ID: SAM
• InChI: InChI=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
• InChIKey: MEFKEPWMEQBLKI-FCKMPRQPSA-N
• SMILES:
  CACTVS 3.341: C[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 1.5.0: C[S+](CCC(C(=O)[O-])N)CC1C(C(C(O1)n2cnc3c2ncnc3N)O)O
  CACTVS 3.341: C[S+](CC[CH](N)C([O-])=O)C[CH]1O[CH]([CH](O)[CH]1O)n2cnc3c(N)ncnc23
  OpenEye OEToolkits 1.5.0: C[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
• Formula: C15 H22 N6 O5 S
• Name: S-ADENOSYLMETHIONINE
• ChEMBL: CHEMBL1235831
• PDB chain: 7yrg Chain L Residue 402

Receptor-Ligand Complex Structure

Structure summary

• PDB: 7yrg Structural insight into H4K20 methylation on H2A.Z-nucleosome by SUV420H1.
• Resolution: 4.2 Å
• Binding residue (original residue number in PDB): H98 Y203 G209 A210 F250 A269 H273 Y307 F312 F318 E320
• Binding residue (residue number reindexed from 1): H37 Y93 G99 A100 F140 A159 H163 Y197 F202 F208 E210
• Annotation score: 5

Enzymatic activity

• Enzyme Commision number: 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:0042799 histone H4K20 methyltransferase activity

External links

• PDB: RCSB:7yrg, PDBe:7yrg, PDBj:7yrg
• PDBsum: 7yrg
• PubMed: 37536340
• UniProt: Q4FZB7|KMT5B_HUMAN Histone-lysine N-methyltransferase KMT5B (Gene Name=KMT5B)