SMTL ID : 8vex.1

Crystal structure of PRMT5:MEP50 in complex with MTA and oxamide compound 28

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.79 Å

Oligo State

hetero-1-1-mer

Ligands

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

MTA.1: 16 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, C.457 Ligands: 01.2, CL.4 9 PLIP interactions: 9 interactions with chain A Hydrogen bonds: A:Y.332, A:Y.332, A:G.375, A:K.401, A:N.402, A:D.427, A:M.428, A:R.429 pi-Cation interactions: A:K.401

1 x 01: N-(6-amino-5-methylpyridin-3-yl)-2-[(2R,5S)-2-(4-hydroxyphenyl)-5-methylpiperidin-1-yl]-2-oxoacetamide

01.2: 16 residues within 4Å: Chain A: Q.317, S.318, L.320, F.335, E.443, L.444, L.445, G.446, S.447, E.452, V.511, F.585, S.586, W.587, F.588 Ligands: MTA.1 13 PLIP interactions: 13 interactions with chain A Hydrophobic interactions: A:L.320, A:L.320, A:F.335, A:F.335, A:E.443, A:W.587, A:F.588 Hydrogen bonds: A:S.318, A:S.447, A:E.452, A:S.586, A:F.588 pi-Stacking: A:W.587

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

CL.3: 2 residues within 4Å: Chain A: L.127, S.157 Ligand excluded by PLIP CL.4: 5 residues within 4Å: Chain A: E.336, Y.342, P.378, E.443 Ligands: MTA.1 Ligand excluded by PLIP

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.5: 3 residues within 4Å: Chain A: I.150, H.154, R.209 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:H.154, A:H.155, A:R.209

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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