SMTL ID : 8vey.1

Crystal structure of PRMT5:MEP50 in complex with MTA and TNG908

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.44 Å

Oligo State

hetero-1-1-mer

Ligands

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

MTA.1: 17 residues within 4Å: Chain A: P.322, L.323, Y.332, F.335, G.373, G.375, E.400, K.401, N.402, S.426, D.427, M.428, R.429, E.443, L.444, C.457 Ligands: 01.2 9 PLIP interactions: 9 interactions with chain A Hydrogen bonds: A:Y.332, A:Y.332, A:G.375, A:K.401, A:D.427, A:M.428 Water bridges: A:N.402, A:N.402 pi-Cation interactions: A:K.401

1 x 01: N-(6-amino-5-methylpyridin-3-yl)-2-[(2R,5S)-2-(1,3-benzothiazol-5-yl)-5-methylpiperidin-1-yl]-2-oxoacetamide

01.2: 17 residues within 4Å: Chain A: F.308, Q.317, S.318, L.320, V.334, F.335, K.341, E.443, L.445, S.447, E.452, V.511, F.585, S.586, W.587, F.588 Ligands: MTA.1 12 PLIP interactions: 12 interactions with chain A Hydrophobic interactions: A:F.308, A:L.320, A:L.320, A:V.334, A:F.335, A:F.335, A:F.335, A:F.588 Hydrogen bonds: A:Q.317, A:E.452, A:S.586, A:F.588

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

PEG.3: 5 residues within 4Å: Chain A: E.137, D.138, N.139, T.140, N.199 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.139, A:T.140 PEG.4: 4 residues within 4Å: Chain A: S.329, Q.330, E.333, R.376 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:S.329, A:Q.330, A:R.376 PEG.12: 11 residues within 4Å: Chain B: N.198, R.199, I.200, Q.213, I.214, G.215, C.216, G.220, Y.221, P.223, F.238 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:I.200, B:Q.213, B:I.214, B:Y.221 PEG.13: 4 residues within 4Å: Chain B: C.81, S.82, T.121, L.122 No protein-ligand interaction detected (PLIP)

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

EDO.5: 8 residues within 4Å: Chain A: L.119, G.122, A.123, L.127, F.130, H.149, S.157, F.159 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:A.123, A:L.127, A:H.149, A:S.157 EDO.14: 1 residues within 4Å: Chain B: G.84 No protein-ligand interaction detected (PLIP)

6 x CL: CHLORIDE ION(Non-functional Binders)

CL.6: 2 residues within 4Å: Chain A: Y.543, T.545 Ligand excluded by PLIP CL.7: 1 residues within 4Å: Chain A: Q.117 Ligand excluded by PLIP CL.8: 5 residues within 4Å: Chain A: R.228, L.230, S.484, H.518, T.554 Ligand excluded by PLIP CL.9: 3 residues within 4Å: Chain A: F.527, T.528, R.542 Ligand excluded by PLIP CL.10: 4 residues within 4Å: Chain A: E.475, Y.476, T.477, E.564 Ligand excluded by PLIP CL.11: 1 residues within 4Å: Chain A: Q.271 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Cottrell, K.M. et al., Discovery of TNG908: A Selective, Brain Penetrant, MTA-Cooperative PRMT5 Inhibitor That Is Synthetically Lethal with MTAP -Deleted Cancers. J.Med.Chem. (2024)

Release Date

2024-04-24

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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