SMTL ID : 9dod.1

Crystal structure of PRMT5:MEP50 in complex with PRT543

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.50 Å

Oligo State

hetero-1-1-mer

Ligands

1 x 01: 7-[(3xi,5R)-5-C-(3,4-dichlorophenyl)-3-C-methyl-beta-D-ribofuranosyl]-7H-pyrrolo[2,3-d]pyrimidin-4-amine

01.1: 17 residues within 4Å: Chain A: P.313, L.314, L.318, Y.323, F.326, K.332, G.364, G.366, E.391, K.392, N.393, S.417, D.418, M.419, E.434, L.435, C.448 18 PLIP interactions: 18 interactions with chain A Hydrophobic interactions: A:P.313, A:L.314, A:L.318, A:Y.323, A:K.392 Hydrogen bonds: A:Y.323, A:Y.323, A:G.366, A:E.391, A:K.392, A:D.418, A:M.419, A:E.434 Water bridges: A:K.392, A:E.443 pi-Stacking: A:Y.323 pi-Cation interactions: A:K.392 Halogen bonds: A:Y.323

4 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.2: 5 residues within 4Å: Chain A: F.326, L.436, S.438, E.443, W.578 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:S.438, A:S.438 Water bridges: A:L.436, A:E.443 EDO.3: 6 residues within 4Å: Chain A: E.128, D.129, N.130, T.131, N.190, L.194 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:D.129, A:N.130, A:T.131, A:T.131 Water bridges: A:E.128 EDO.4: 5 residues within 4Å: Chain A: K.332, Y.336, E.434, L.436, W.578 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:K.332, A:Y.336 Water bridges: A:L.436 EDO.5: 3 residues within 4Å: Chain A: D.69, L.72, G.74 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Bewersdorf, J.P. et al., Phase Ib study of PRT543, an oral protein arginine methyltransferase 5 (PRMT5) inhibitor, in patients with advanced splicing factor-mutant myeloid malignancies. Leukemia (2025)

Release Date

2025-02-12

Peptides

Protein arginine N-methyltransferase 5: A
Methylosome protein WDR77: B

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Protein arginine N-methyltransferase 5

Methylosome protein WDR77