SMTL ID : 7m05.1

CryoEM structure of PRMT5 bound to covalent PBM-site inhibitor BRD-6988

Coordinates

PDB Format

Method

ELECTRON MICROSCOPY

Oligo State

hetero-4-4-mer

Ligands

4 x YJG: 2-(5-chloro-6-oxopyridazin-1(6H)-yl)-N-(4-methyl-3-{[2-(pyridin-2-yl)ethyl]sulfamoyl}phenyl)acetamide(Covalent)

YJG.1: 11 residues within 4Å: Chain A: N.239, K.241, F.243, P.244, V.245, E.276, C.278, S.279, Q.282, Y.283, Y.286 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:F.243, A:V.245, A:Y.283, A:Y.286 Hydrogen bonds: A:N.239, A:K.241 YJG.2: 11 residues within 4Å: Chain C: N.239, K.241, F.243, P.244, V.245, E.276, C.278, S.279, Q.282, Y.283, Y.286 6 PLIP interactions: 6 interactions with chain C Hydrophobic interactions: C:F.243, C:V.245, C:Y.283, C:Y.286 Hydrogen bonds: C:N.239, C:K.241 YJG.3: 11 residues within 4Å: Chain E: N.239, K.241, F.243, P.244, V.245, E.276, C.278, S.279, Q.282, Y.283, Y.286 6 PLIP interactions: 6 interactions with chain E Hydrophobic interactions: E:F.243, E:V.245, E:Y.283, E:Y.286 Hydrogen bonds: E:N.239, E:K.241 YJG.4: 11 residues within 4Å: Chain G: N.239, K.241, F.243, P.244, V.245, E.276, C.278, S.279, Q.282, Y.283, Y.286 6 PLIP interactions: 6 interactions with chain G Hydrophobic interactions: G:F.243, G:V.245, G:Y.283, G:Y.286 Hydrogen bonds: G:N.239, G:K.241

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

McKinney, D.C. et al., Discovery of a First-in-Class Inhibitor of the PRMT5-Substrate Adaptor Interaction. J.Med.Chem. (2021)

Release Date

2021-03-17

Peptides

Protein arginine N-methyltransferase 5: ACEG
Methylosome protein 50: BDFH

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

C
C

E
E

G
G

B
B

D
D

F
F

H
H

Protein arginine N-methyltransferase 5

Methylosome protein 50

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