SMTL ID : 8vew.1

Crystal structure of PRMT5:MEP50 in complex with MTA and oxamide compound 24

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.69 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, E.443, L.444, C.457 10 PLIP interactions: 10 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 Water bridges: A:N.402 pi-Cation interactions: A:K.401

1 x 01: 5-{2-[(2R,5S)-5-methyl-2-phenylpiperidin-1-yl](oxo)acetamido}pyridine-3-carboxamide

01.2: 13 residues within 4Å: Chain A: Q.317, S.318, L.320, F.335, K.341, E.443, L.445, S.447, E.452, V.511, S.586, W.587, F.588 12 PLIP interactions: 12 interactions with chain A Hydrophobic interactions: A:Q.317, A:L.320, A:L.320, A:L.320, A:W.587, A:F.588 Hydrogen bonds: A:E.443, A:S.586, A:S.586, A:F.588 pi-Stacking: A:F.335, A:W.587

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.3: 6 residues within 4Å: Chain A: I.150, H.151, H.154, S.207, K.208, R.209 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:H.154, A:S.207, A:R.209

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

CL.4: 4 residues within 4Å: Chain A: G.122, A.123, S.157, F.159 Ligand excluded by PLIP CL.5: 6 residues within 4Å: Chain A: D.227, R.228, L.230, S.484, H.518, T.554 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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