SMTL ID : 9n3r.1

Crystal structure of PRMT5:MEP50 in complex with MTA and TNG462

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.47 Å

Oligo State

hetero-4-4-mer

Ligands

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

MTA.1: 16 residues within 4Å: Chain A: P.322, L.323, Y.332, 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 8 PLIP interactions: 8 interactions with chain A Hydrogen bonds: A:Y.332, A:G.375, A:K.401, A:D.427, A:M.428 Water bridges: A:Y.332, A:N.402 pi-Cation interactions: A:K.401 MTA.5: 14 residues within 4Å: Chain C: P.322, L.323, Y.332, G.373, G.375, E.400, K.401, S.426, D.427, M.428, R.429, L.444, C.457 Ligands: 01.6 8 PLIP interactions: 8 interactions with chain C Hydrogen bonds: C:Y.332, C:Y.332, C:G.375, C:K.401, C:D.427, C:M.428 Water bridges: C:N.402 pi-Cation interactions: C:K.401 MTA.12: 16 residues within 4Å: Chain E: P.322, L.323, Y.332, 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: 01.13 8 PLIP interactions: 8 interactions with chain E Hydrogen bonds: E:Y.332, E:G.375, E:K.401, E:D.427, E:M.428 Water bridges: E:Y.332, E:N.402 pi-Cation interactions: E:K.401 MTA.16: 14 residues within 4Å: Chain G: P.322, L.323, Y.332, G.373, G.375, E.400, K.401, S.426, D.427, M.428, R.429, L.444, C.457 Ligands: 01.17 8 PLIP interactions: 8 interactions with chain G Hydrogen bonds: G:Y.332, G:Y.332, G:G.375, G:K.401, G:D.427, G:M.428 Water bridges: G:N.402 pi-Cation interactions: G:K.401

4 x 01: N-(6-amino-5-ethylpyridin-3-yl)-2-{(2R,5S)-5-methyl-2-[2-(1-methylpiperidin-4-yl)-1,3-benzothiazol-5-yl]piperidin-1-yl}-2-oxoacetamide

01.2: 17 residues within 4Å: Chain A: Q.317, S.318, L.320, E.328, V.334, F.335, K.341, E.443, L.445, S.447, E.452, V.511, S.586, W.587, F.588 Chain C: H.155 Ligands: MTA.1 13 PLIP interactions: 13 interactions with chain A Hydrophobic interactions: A:L.320, A:L.320, A:V.334, A:F.335, A:F.335, A:W.587, A:F.588 Hydrogen bonds: A:Q.317, A:E.452, A:S.586, A:F.588 Salt bridges: A:E.328 pi-Stacking: A:W.587 01.6: 17 residues within 4Å: Chain A: H.155 Chain C: Q.317, S.318, L.320, E.328, V.334, F.335, K.341, E.443, L.445, S.447, E.452, V.511, S.586, W.587, F.588 Ligands: MTA.5 13 PLIP interactions: 13 interactions with chain C Hydrophobic interactions: C:L.320, C:L.320, C:V.334, C:F.335, C:F.335, C:E.443, C:W.587, C:F.588 Hydrogen bonds: C:Q.317, C:E.452, C:S.586, C:F.588 Salt bridges: C:E.328 01.13: 17 residues within 4Å: Chain E: Q.317, S.318, L.320, E.328, V.334, F.335, K.341, E.443, L.445, S.447, E.452, V.511, S.586, W.587, F.588 Chain G: H.155 Ligands: MTA.12 13 PLIP interactions: 13 interactions with chain E Hydrophobic interactions: E:L.320, E:L.320, E:V.334, E:F.335, E:F.335, E:W.587, E:F.588 Hydrogen bonds: E:Q.317, E:E.452, E:S.586, E:F.588 Salt bridges: E:E.328 pi-Stacking: E:W.587 01.17: 17 residues within 4Å: Chain E: H.155 Chain G: Q.317, S.318, L.320, E.328, V.334, F.335, K.341, E.443, L.445, S.447, E.452, V.511, S.586, W.587, F.588 Ligands: MTA.16 13 PLIP interactions: 13 interactions with chain G Hydrophobic interactions: G:L.320, G:L.320, G:V.334, G:F.335, G:F.335, G:E.443, G:W.587, G:F.588 Hydrogen bonds: G:Q.317, G:E.452, G:S.586, G:F.588 Salt bridges: G:E.328

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

CL.3: 1 residues within 4Å: Chain A: T.642 Ligand excluded by PLIP CL.4: 3 residues within 4Å: Chain A: R.99, D.101, Q.136 Ligand excluded by PLIP CL.7: 5 residues within 4Å: Chain C: R.228, L.230, S.484, H.518, T.554 Ligand excluded by PLIP CL.8: 3 residues within 4Å: Chain C: E.475, T.477, E.564 Ligand excluded by PLIP CL.9: 4 residues within 4Å: Chain C: I.226, W.229, L.230, R.264 Ligand excluded by PLIP CL.14: 1 residues within 4Å: Chain E: T.642 Ligand excluded by PLIP CL.15: 3 residues within 4Å: Chain E: R.99, D.101, Q.136 Ligand excluded by PLIP CL.18: 5 residues within 4Å: Chain G: R.228, L.230, S.484, H.518, T.554 Ligand excluded by PLIP CL.19: 3 residues within 4Å: Chain G: E.475, T.477, E.564 Ligand excluded by PLIP CL.20: 4 residues within 4Å: Chain G: I.226, W.229, L.230, R.264 Ligand excluded by PLIP

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

EDO.10: 5 residues within 4Å: Chain C: C.526, F.527, R.542, Y.543, C.544 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:C.526, C:Y.543 EDO.11: 6 residues within 4Å: Chain D: N.198, I.200, I.214, G.215, C.216, Y.221 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:I.200 EDO.21: 5 residues within 4Å: Chain G: C.526, F.527, R.542, Y.543, C.544 2 PLIP interactions: 2 interactions with chain G Hydrogen bonds: G:C.526, G:Y.543 EDO.22: 6 residues within 4Å: Chain H: N.198, I.200, I.214, G.215, C.216, Y.221 1 PLIP interactions: 1 interactions with chain H Hydrogen bonds: H:I.200

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Cottrell, K.M. et al., Discovery of TNG462: A Highly Potent and Selective MTA-Cooperative PRMT5 Inhibitor to Target Cancers with MTAP Deletion. J.Med.Chem. (2025)

Release Date

2025-03-12

Peptides

Protein arginine N-methyltransferase 5: ACEG
Methylosome protein 50: BDFH

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

C
C

E
A

G
C

B
B

D
D

F
B

H
D

Protein arginine N-methyltransferase 5

Methylosome protein 50

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