SMTL ID : 8cyi.1

Cryo-EM structures and computational analysis for enhanced potency in MTA-synergic inhibition of human protein arginine methyltransferase 5

Coordinates

PDB Format

Method

ELECTRON MICROSCOPY 3.14 Å

Oligo State

hetero-1-1-mer

Ligands

1 x P2R: N-[(2-aminoquinolin-7-yl)methyl]-9-(2-hydroxyethyl)-2,3,4,9-tetrahydro-1H-carbazole-6-carboxamide(Non-covalent)

P2R.1: 21 residues within 4Å: Chain A: Q.309, S.310, P.311, L.312, P.314, Q.322, T.323, V.326, F.327, K.333, E.435, L.436, L.437, G.438, S.439, E.444, V.503, S.578, W.579, F.580 Ligands: MTA.2 9 PLIP interactions: 9 interactions with chain A Hydrophobic interactions: A:Q.309, A:L.312, A:L.312, A:V.326, A:F.327 Hydrogen bonds: A:L.312, A:E.435 pi-Stacking: A:F.327, A:W.579

1 x MTA: 5'-DEOXY-5'-METHYLTHIOADENOSINE(Non-covalent)

MTA.2: 19 residues within 4Å: Chain A: P.314, L.315, L.319, Y.324, F.327, G.365, G.367, V.391, E.392, K.393, N.394, S.418, D.419, M.420, R.421, E.435, L.436, C.449 Ligands: P2R.1 8 PLIP interactions: 8 interactions with chain A Hydrogen bonds: A:Y.324, A:G.365, A:G.367, A:E.392, A:K.393, A:D.419, A:M.420 pi-Cation interactions: A:K.393

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Zhou, W. et al., Cryo-EM structure-based selection of computed ligand poses enables design of MTA-synergic PRMT5 inhibitors of better potency. Commun Biol (2022)

Release Date

2023-04-12

Peptides

Protein arginine N-methyltransferase 5: A
Methylosome protein 50: B

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Protein arginine N-methyltransferase 5

Methylosome protein 50

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