Structure of PDB 8d59 Chain A Binding Site BS01

Receptor Information

>8d59 Chain A (length=201) Species: 9606 (Homo sapiens)

YPVKPEEMDWSELYPEFFQAQVEFADIGCGYGGLLVELSPLFPDTLILGL
EIRVKVSDYVQDRIRALRAAPAGGFQNIACLRSNAMKHLPNFFYKGQLTK
MFFLFPDPWRIISPTLLAEYAYVLRVGGLVYTITDVLELHDWMCTHFEEH
PLFERVPLEDLSEDPVVGHLGTSTEEGKKVLRNGGKNFPAIFRRIQDPVL
Q

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: 8d59 Chain A Residue 301

Receptor-Ligand Complex Structure

Structure summary

• PDB: 8d59 Structures and mechanisms of tRNA methylation by METTL1-WDR4.
• Resolution: 2.26 Å
• Binding residue (original residue number in PDB): G84 C85 E107 I108 R109 N140 A141 L160 F161 T238 E240
• Binding residue (residue number reindexed from 1): G28 C29 E51 I52 R53 N84 A85 L104 F105 T174 E176
• Annotation score: 5

Enzymatic activity

• Enzyme Commision number: 2.1.1.-
  2.1.1.33: tRNA (guanine(46)-N(7))-methyltransferase.

Gene Ontology

Molecular Function

• GO:0008176 tRNA (guanine(46)-N7)-methyltransferase activity

Biological Process

• GO:0006400 tRNA modification

External links

• PDB: RCSB:8d59, PDBe:8d59, PDBj:8d59
• PDBsum: 8d59
• PubMed: 36599982
• UniProt: Q9UBP6|TRMB_HUMAN tRNA (guanine-N(7)-)-methyltransferase (Gene Name=METTL1)