› 9n3o

X-ray diffraction
2.37Å resolution

Crystal structure of PRMT5:MEP50 in complex with MTA and oxamide compound 14

Released:
DOI: 10.2210/pdb9n3o/pdb
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PDB entry 9n3o coloured by chain, front view.
PDB entry 9n3o coloured by chain, side view.
PDB entry 9n3o coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
Discovery of TNG462: A Highly Potent and Selective MTA-Cooperative PRMT5 Inhibitor to Target Cancers with MTAP Deletion.
Cottrell KM, Briggs KJ, Tsai A, Tonini MR, Whittington DA, Gong S, Liang C, McCarren P, Zhang M, Zhang W, Huang A, Maxwell JP
J Med Chem (2025)
PMID: 40035511

Function and Biology Details

Reaction catalysed: 
(1a) S-adenosyl-L-methionine + [protein]-L-arginine = S-adenosyl-L-homocysteine + [protein]-N(omega)-methyl-L-arginine
Biochemical function:
  • not assigned
Biological process:
  • not assigned
Cellular component:
  • not assigned

Structure analysis Details

Assembly composition:
hetero octamer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-127081 (preferred)
Entry contents:
2 distinct polypeptide molecules
Macromolecules (2 distinct):
Protein arginine N-methyltransferase 5 Chain: A
Molecule details ›
Chain: A
Length: 645 amino acids
Theoretical weight: 73.76 KDa
Source organism: Homo sapiens
Expression system: Trichoplusia ni
UniProt:
  • Canonical: O14744 (Residues: 2-637; Coverage: 100%)
Gene names: HRMT1L5, IBP72, JBP1, PRMT5, SKB1
Sequence domains:
Methylosome protein WDR77 Chain: B
Molecule details ›
Chain: B
Length: 350 amino acids
Theoretical weight: 37.86 KDa
Source organism: Homo sapiens
Expression system: Trichoplusia ni
UniProt:
  • Canonical: Q9BQA1 (Residues: 2-342; Coverage: 100%)
Gene names: HKMT1069, MEP50, Nbla10071, WD45, WDR77
Sequence domains: WD domain, G-beta repeat

Ligands and Environments

5 bound ligands:
Ligand MTA 1 x MTA
Ligand A1BV4 1 x A1BV4
Ligand CL 2 x CL
Ligand EDO 10 x EDO
Ligand GOL 1 x GOL
No modified residues

Experiments and Validation Details

wwPDB Validation report is not available for this entry.
X-ray source: CLSI BEAMLINE 08B1-1
Spacegroup: I222
Unit cell:
a: 101.76Å b: 137.2Å c: 176.84Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.196 0.194 0.227
Expression system: Trichoplusia ni

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