SMTL ID : 9n3p.1

Crystal structure of PRMT5:MEP50 in complex with MTA and oxamide compound 30

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.51 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, F.335, G.373, G.375, E.400, K.401, 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:Y.332, A:G.375, A:K.401, A:D.427, A:M.428 Water bridges: A:N.402 pi-Cation interactions: A:K.401 MTA.13: 16 residues within 4Å: Chain C: P.322, L.323, Y.332, F.335, G.373, G.375, E.400, K.401, S.426, D.427, M.428, R.429, E.443, L.444, C.457 Ligands: 01.14 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.25: 16 residues within 4Å: Chain E: P.322, L.323, Y.332, F.335, G.373, G.375, E.400, K.401, S.426, D.427, M.428, R.429, E.443, L.444, C.457 Ligands: 01.26 7 PLIP interactions: 7 interactions with chain E Hydrogen bonds: E:Y.332, E:G.375, E:K.401, E:D.427, E:M.428 Water bridges: E:N.402 pi-Cation interactions: E:K.401 MTA.37: 16 residues within 4Å: Chain G: P.322, L.323, Y.332, F.335, G.373, G.375, E.400, K.401, S.426, D.427, M.428, R.429, E.443, L.444, C.457 Ligands: 01.38 7 PLIP interactions: 7 interactions with chain G Hydrogen bonds: 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

8 x 01: N-(6-amino-5-methylpyridin-3-yl)-2-[(2S,5R)-2-(4-fluorophenyl)-5-methyl-4-(2-methylpropanoyl)piperazin-1-yl]-2-oxoacetamide

01.2: 17 residues within 4Å: Chain A: F.308, Y.312, Q.317, S.318, L.320, V.334, F.335, E.443, L.445, S.447, E.452, V.511, F.585, S.586, W.587, F.588 Ligands: MTA.1 15 PLIP interactions: 15 interactions with chain A Hydrophobic interactions: A:F.308, A:Y.312, A:Y.312, A:L.320, A:L.320, A:E.443, A:W.587, A:F.588, A:F.588 Hydrogen bonds: A:E.452, A:S.586, A:F.588 Water bridges: A:L.320, A:S.447 pi-Stacking: A:F.335 01.10: 14 residues within 4Å: Chain B: R.43, Y.44, R.45, S.46, P.230, V.270, F.271, S.272, P.273, D.310, A.311, T.312, W.313, P.315 7 PLIP interactions: 7 interactions with chain B Hydrophobic interactions: B:P.273 Hydrogen bonds: B:T.312, B:W.313 Water bridges: B:R.43, B:R.43, B:L.94, B:D.310 01.14: 17 residues within 4Å: Chain C: F.308, Y.312, Q.317, S.318, L.320, V.334, F.335, E.443, L.445, S.447, E.452, V.511, F.585, S.586, W.587, F.588 Ligands: MTA.13 15 PLIP interactions: 15 interactions with chain C Hydrophobic interactions: C:F.308, C:Y.312, C:Y.312, C:L.320, C:L.320, C:E.443, C:W.587, C:F.588, C:F.588 Hydrogen bonds: C:E.452, C:S.586, C:F.588 Water bridges: C:L.320, C:S.447 pi-Stacking: C:F.335 01.22: 14 residues within 4Å: Chain D: R.43, Y.44, R.45, S.46, P.230, V.270, F.271, S.272, P.273, D.310, A.311, T.312, W.313, P.315 7 PLIP interactions: 7 interactions with chain D Hydrophobic interactions: D:P.273 Hydrogen bonds: D:T.312, D:W.313 Water bridges: D:R.43, D:R.43, D:L.94, D:D.310 01.26: 17 residues within 4Å: Chain E: F.308, Y.312, Q.317, S.318, L.320, V.334, F.335, E.443, L.445, S.447, E.452, V.511, F.585, S.586, W.587, F.588 Ligands: MTA.25 15 PLIP interactions: 15 interactions with chain E Hydrophobic interactions: E:F.308, E:Y.312, E:Y.312, E:L.320, E:L.320, E:E.443, E:W.587, E:F.588, E:F.588 Hydrogen bonds: E:E.452, E:S.586, E:F.588 Water bridges: E:L.320, E:S.447 pi-Stacking: E:F.335 01.34: 14 residues within 4Å: Chain F: R.43, Y.44, R.45, S.46, P.230, V.270, F.271, S.272, P.273, D.310, A.311, T.312, W.313, P.315 6 PLIP interactions: 6 interactions with chain F Hydrophobic interactions: F:P.273 Hydrogen bonds: F:W.313 Water bridges: F:R.43, F:R.43, F:L.94, F:D.310 01.38: 17 residues within 4Å: Chain G: F.308, Y.312, Q.317, S.318, L.320, V.334, F.335, E.443, L.445, S.447, E.452, V.511, F.585, S.586, W.587, F.588 Ligands: MTA.37 15 PLIP interactions: 15 interactions with chain G Hydrophobic interactions: G:F.308, G:Y.312, G:Y.312, G:L.320, G:L.320, G:E.443, G:W.587, G:F.588, G:F.588 Hydrogen bonds: G:E.452, G:S.586, G:F.588 Water bridges: G:L.320, G:S.447 pi-Stacking: G:F.335 01.46: 14 residues within 4Å: Chain H: R.43, Y.44, R.45, S.46, P.230, V.270, F.271, S.272, P.273, D.310, A.311, T.312, W.313, P.315 6 PLIP interactions: 6 interactions with chain H Hydrophobic interactions: H:P.273 Hydrogen bonds: H:W.313 Water bridges: H:R.43, H:R.43, H:L.94, H:D.310

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

EDO.3: 6 residues within 4Å: Chain A: W.194, R.228, L.230, S.484, H.518, T.554 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:W.194, A:R.228, A:S.484, A:H.518 EDO.11: 3 residues within 4Å: Chain B: H.274, S.275, H.318 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:S.275, B:S.275 EDO.15: 6 residues within 4Å: Chain C: W.194, R.228, L.230, S.484, H.518, T.554 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:W.194, C:R.228, C:S.484, C:H.518 EDO.23: 3 residues within 4Å: Chain D: H.274, S.275, H.318 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:S.275, D:S.275 EDO.27: 6 residues within 4Å: Chain E: W.194, R.228, L.230, S.484, H.518, T.554 5 PLIP interactions: 5 interactions with chain E Hydrogen bonds: E:W.194, E:R.228, E:S.484, E:H.518, E:T.554 EDO.35: 3 residues within 4Å: Chain F: H.274, S.275, H.318 4 PLIP interactions: 4 interactions with chain F Hydrogen bonds: F:H.274, F:S.275, F:S.275, F:H.318 EDO.39: 6 residues within 4Å: Chain G: W.194, R.228, L.230, S.484, H.518, T.554 5 PLIP interactions: 5 interactions with chain G Hydrogen bonds: G:W.194, G:R.228, G:S.484, G:H.518, G:T.554 EDO.47: 3 residues within 4Å: Chain H: H.274, S.275, H.318 4 PLIP interactions: 4 interactions with chain H Hydrogen bonds: H:H.274, H:S.275, H:S.275, H:H.318

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

CL.4: 3 residues within 4Å: Chain A: G.83, W.86 Chain G: S.329 Ligand excluded by PLIP CL.5: 1 residues within 4Å: Chain A: Q.271 Ligand excluded by PLIP CL.6: 4 residues within 4Å: Chain A: G.122, A.123, L.127, S.157 Ligand excluded by PLIP CL.7: 4 residues within 4Å: Chain A: E.336, R.376, W.412 Chain G: L.79 Ligand excluded by PLIP CL.8: 2 residues within 4Å: Chain A: Q.117 Chain G: P.403 Ligand excluded by PLIP CL.9: 4 residues within 4Å: Chain A: R.109 Chain C: N.541, R.542, Y.543 Ligand excluded by PLIP CL.12: 3 residues within 4Å: Chain B: N.198, G.215, C.216 Ligand excluded by PLIP CL.16: 3 residues within 4Å: Chain C: G.83, W.86 Chain E: S.329 Ligand excluded by PLIP CL.17: 1 residues within 4Å: Chain C: Q.271 Ligand excluded by PLIP CL.18: 4 residues within 4Å: Chain C: G.122, A.123, L.127, S.157 Ligand excluded by PLIP CL.19: 4 residues within 4Å: Chain C: E.336, R.376, W.412 Chain E: L.79 Ligand excluded by PLIP CL.20: 2 residues within 4Å: Chain C: Q.117 Chain E: P.403 Ligand excluded by PLIP CL.21: 4 residues within 4Å: Chain A: N.541, R.542, Y.543 Chain C: R.109 Ligand excluded by PLIP CL.24: 3 residues within 4Å: Chain D: N.198, G.215, C.216 Ligand excluded by PLIP CL.28: 3 residues within 4Å: Chain C: S.329 Chain E: G.83, W.86 Ligand excluded by PLIP CL.29: 1 residues within 4Å: Chain E: Q.271 Ligand excluded by PLIP CL.30: 4 residues within 4Å: Chain E: G.122, A.123, L.127, S.157 Ligand excluded by PLIP CL.31: 4 residues within 4Å: Chain C: L.79 Chain E: E.336, R.376, W.412 Ligand excluded by PLIP CL.32: 2 residues within 4Å: Chain C: P.403 Chain E: Q.117 Ligand excluded by PLIP CL.33: 4 residues within 4Å: Chain E: R.109 Chain G: N.541, R.542, Y.543 Ligand excluded by PLIP CL.36: 3 residues within 4Å: Chain F: N.198, G.215, C.216 Ligand excluded by PLIP CL.40: 3 residues within 4Å: Chain A: S.329 Chain G: G.83, W.86 Ligand excluded by PLIP CL.41: 1 residues within 4Å: Chain G: Q.271 Ligand excluded by PLIP CL.42: 4 residues within 4Å: Chain G: G.122, A.123, L.127, S.157 Ligand excluded by PLIP CL.43: 4 residues within 4Å: Chain A: L.79 Chain G: E.336, R.376, W.412 Ligand excluded by PLIP CL.44: 2 residues within 4Å: Chain A: P.403 Chain G: Q.117 Ligand excluded by PLIP CL.45: 4 residues within 4Å: Chain E: N.541, R.542, Y.543 Chain G: R.109 Ligand excluded by PLIP CL.48: 3 residues within 4Å: Chain H: N.198, G.215, C.216 Ligand excluded by PLIP

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
A

E
A

G
A

B
B

D
B

F
B

H
B

Protein arginine N-methyltransferase 5

Methylosome protein 50

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