SMTL ID : 9mre.1

From DNA-Encoded Library Screening to AM-9747 - an MTA-Cooperative PRMT5 Inhibitor with Potent Oral in vivo Efficacy

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.25 Å

Oligo State

hetero-1-1-mer

Ligands

1 x 01: 2-amino-3-methyl-N-[(1R)-1-(pyrimidin-2-yl)ethyl]-N-{[5-(trifluoromethyl)pyridin-2-yl]methyl}quinoline-6-carboxamide

01.1: 18 residues within 4Å: Chain A: F.313, Y.317, Q.322, S.323, L.325, V.339, F.340, K.346, E.448, L.450, S.452, E.457, V.516, F.590, S.591, W.592, F.593 Ligands: MTA.2 12 PLIP interactions: 12 interactions with chain A Hydrophobic interactions: A:Q.322, A:L.325, A:V.339, A:F.340 Hydrogen bonds: A:E.457, A:F.593 Water bridges: A:Q.322, A:L.325, A:L.450 pi-Stacking: A:Y.317, A:F.340, A:F.593

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

MTA.2: 17 residues within 4Å: Chain A: P.327, L.328, Y.337, F.340, G.378, G.380, E.405, K.406, N.407, S.431, D.432, M.433, R.434, E.448, L.449, C.462 Ligands: 01.1 8 PLIP interactions: 8 interactions with chain A Hydrogen bonds: A:Y.337, A:Y.337, A:G.380, A:K.406, A:D.432, A:M.433 Water bridges: A:N.407 pi-Cation interactions: A:K.406

5 x GOL: GLYCEROL(Non-functional Binders)

GOL.3: 5 residues within 4Å: Chain A: G.643, R.644, S.645, T.647 Ligands: GOL.4 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:G.643 Water bridges: A:R.644, A:S.645 GOL.4: 6 residues within 4Å: Chain A: Q.326, M.513, S.645, Y.646, T.647 Ligands: GOL.3 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:Q.326, A:T.647 Water bridges: A:T.647, A:T.647 GOL.5: 5 residues within 4Å: Chain A: R.381, G.382, P.383, N.386, W.417 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.381, A:N.386 GOL.7: 5 residues within 4Å: Chain A: F.53, T.93, P.133, W.165, Q.276 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:T.93, A:Q.276 GOL.11: 4 residues within 4Å: Chain A: D.83, L.84, L.86, G.88 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:D.83

3 x PEG: DI(HYDROXYETHYL)ETHER(Non-functional Binders)

PEG.6: 6 residues within 4Å: Chain A: E.142, D.143, N.144, T.145, N.204, L.208 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:E.142, A:E.142, A:N.144, A:N.204 Water bridges: A:N.144 PEG.9: 3 residues within 4Å: Chain A: A.47, D.90, L.94 No protein-ligand interaction detected (PLIP) PEG.12: 2 residues within 4Å: Chain B: N.71, G.73 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:N.71

3 x DMS: DIMETHYL SULFOXIDE(Non-functional Binders)

DMS.8: 2 residues within 4Å: Chain A: G.316, Y.317 2 PLIP interactions: 2 interactions with chain A pi-Cation interactions: A:Y.317, A:Y.320 DMS.10: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) DMS.13: 7 residues within 4Å: Chain B: N.192, I.194, C.210, G.214, Y.215, P.217, F.232 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:N.192, B:G.214

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Sarvary, I. et al., From DNA-Encoded Library Screening to AM-9747 : An MTA-Cooperative PRMT5 Inhibitor with Potent Oral In Vivo Efficacy. J.Med.Chem. (2025)

Release Date

2025-03-26

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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