SMTL ID : 9n3o.1

Crystal structure of PRMT5:MEP50 in complex with MTA and oxamide compound 14

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.37 Å

Oligo State

hetero-4-4-mer

Ligands

4 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 MTA.16: 17 residues within 4Å: Chain C: 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: 01.17 9 PLIP interactions: 9 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, C:N.402 pi-Cation interactions: C:K.401 MTA.31: 17 residues within 4Å: Chain E: 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: 01.32 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:N.402, E:N.402 pi-Cation interactions: E:K.401 MTA.46: 17 residues within 4Å: Chain G: 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: 01.47 8 PLIP interactions: 8 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, G:N.402 pi-Cation interactions: G:K.401

4 x 01: N-(4-amino-1H-pyrazolo[4,3-c]pyridin-7-yl)-2-[(2R,5S)-2-(1,3-benzothiazol-5-yl)-5-methylpiperidin-1-yl]-2-oxoacetamide

01.2: 15 residues within 4Å: Chain A: Q.317, S.318, L.320, V.334, F.335, K.341, E.443, L.445, E.452, V.511, F.585, S.586, W.587, F.588 Ligands: MTA.1 17 PLIP interactions: 17 interactions with chain A Hydrophobic interactions: A:Q.317, A:L.320, A:L.320, A:V.334, A:F.588 Hydrogen bonds: A:Q.317, A:K.341, A:L.445, A:E.452, A:S.586, A:S.586, A:F.588 pi-Stacking: A:F.335, A:F.335, A:W.587, A:W.587, A:W.587 01.17: 15 residues within 4Å: Chain C: Q.317, S.318, L.320, V.334, F.335, K.341, E.443, L.445, E.452, V.511, F.585, S.586, W.587, F.588 Ligands: MTA.16 17 PLIP interactions: 17 interactions with chain C Hydrophobic interactions: C:Q.317, C:L.320, C:L.320, C:V.334, C:F.588 Hydrogen bonds: C:Q.317, C:K.341, C:L.445, C:E.452, C:S.586, C:S.586, C:F.588 pi-Stacking: C:F.335, C:F.335, C:W.587, C:W.587, C:W.587 01.32: 15 residues within 4Å: Chain E: Q.317, S.318, L.320, V.334, F.335, K.341, E.443, L.445, E.452, V.511, F.585, S.586, W.587, F.588 Ligands: MTA.31 17 PLIP interactions: 17 interactions with chain E Hydrophobic interactions: E:Q.317, E:L.320, E:L.320, E:V.334, E:F.588 Hydrogen bonds: E:Q.317, E:K.341, E:L.445, E:E.452, E:S.586, E:S.586, E:F.588 pi-Stacking: E:F.335, E:F.335, E:W.587, E:W.587, E:W.587 01.47: 15 residues within 4Å: Chain G: Q.317, S.318, L.320, V.334, F.335, K.341, E.443, L.445, E.452, V.511, F.585, S.586, W.587, F.588 Ligands: MTA.46 17 PLIP interactions: 17 interactions with chain G Hydrophobic interactions: G:Q.317, G:L.320, G:L.320, G:V.334, G:F.588 Hydrogen bonds: G:Q.317, G:K.341, G:L.445, G:E.452, G:S.586, G:S.586, G:F.588 pi-Stacking: G:F.335, G:F.335, G:W.587, G:W.587, G:W.587

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

CL.3: 2 residues within 4Å: Chain A: L.316, Y.510 Ligand excluded by PLIP CL.14: 1 residues within 4Å: Chain B: G.84 Ligand excluded by PLIP CL.18: 2 residues within 4Å: Chain C: L.316, Y.510 Ligand excluded by PLIP CL.29: 1 residues within 4Å: Chain D: G.84 Ligand excluded by PLIP CL.33: 2 residues within 4Å: Chain E: L.316, Y.510 Ligand excluded by PLIP CL.44: 1 residues within 4Å: Chain F: G.84 Ligand excluded by PLIP CL.48: 2 residues within 4Å: Chain G: L.316, Y.510 Ligand excluded by PLIP CL.59: 1 residues within 4Å: Chain H: G.84 Ligand excluded by PLIP

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

EDO.4: 10 residues within 4Å: Chain A: L.119, G.122, A.123, L.127, A.129, F.130, H.149, S.157, M.158, F.159 Ligand excluded by PLIP EDO.5: 6 residues within 4Å: Chain A: P.403, N.404, V.407 Chain G: F.54, Q.74, Q.117 Ligand excluded by PLIP EDO.6: 6 residues within 4Å: Chain A: K.93, L.94, L.131, L.132, P.133, R.162 Ligand excluded by PLIP EDO.7: 7 residues within 4Å: Chain A: I.226, W.229, L.230, I.234, R.264, L.265, L.268 Ligand excluded by PLIP EDO.8: 7 residues within 4Å: Chain A: W.194, D.227, R.228, L.230, S.484, H.518, T.554 Ligand excluded by PLIP EDO.9: 7 residues within 4Å: Chain A: P.164, L.165, V.166, L.171, E.215, I.216, G.217 Ligand excluded by PLIP EDO.10: 4 residues within 4Å: Chain A: Y.543, C.544, T.545 Chain C: R.108 Ligand excluded by PLIP EDO.11: 5 residues within 4Å: Chain A: F.48, T.88, P.128, W.160, Q.271 Ligand excluded by PLIP EDO.12: 6 residues within 4Å: Chain A: E.475, Y.476, T.477, E.564, T.565, V.566 Ligand excluded by PLIP EDO.15: 7 residues within 4Å: Chain B: N.198, R.199, I.200, Q.213, I.214, G.215, C.216 Ligand excluded by PLIP EDO.19: 10 residues within 4Å: Chain C: L.119, G.122, A.123, L.127, A.129, F.130, H.149, S.157, M.158, F.159 Ligand excluded by PLIP EDO.20: 6 residues within 4Å: Chain C: P.403, N.404, V.407 Chain E: F.54, Q.74, Q.117 Ligand excluded by PLIP EDO.21: 6 residues within 4Å: Chain C: K.93, L.94, L.131, L.132, P.133, R.162 Ligand excluded by PLIP EDO.22: 7 residues within 4Å: Chain C: I.226, W.229, L.230, I.234, R.264, L.265, L.268 Ligand excluded by PLIP EDO.23: 7 residues within 4Å: Chain C: W.194, D.227, R.228, L.230, S.484, H.518, T.554 Ligand excluded by PLIP EDO.24: 7 residues within 4Å: Chain C: P.164, L.165, V.166, L.171, E.215, I.216, G.217 Ligand excluded by PLIP EDO.25: 4 residues within 4Å: Chain A: R.108 Chain C: Y.543, C.544, T.545 Ligand excluded by PLIP EDO.26: 5 residues within 4Å: Chain C: F.48, T.88, P.128, W.160, Q.271 Ligand excluded by PLIP EDO.27: 6 residues within 4Å: Chain C: E.475, Y.476, T.477, E.564, T.565, V.566 Ligand excluded by PLIP EDO.30: 7 residues within 4Å: Chain D: N.198, R.199, I.200, Q.213, I.214, G.215, C.216 Ligand excluded by PLIP EDO.34: 10 residues within 4Å: Chain E: L.119, G.122, A.123, L.127, A.129, F.130, H.149, S.157, M.158, F.159 Ligand excluded by PLIP EDO.35: 6 residues within 4Å: Chain C: F.54, Q.74, Q.117 Chain E: P.403, N.404, V.407 Ligand excluded by PLIP EDO.36: 6 residues within 4Å: Chain E: K.93, L.94, L.131, L.132, P.133, R.162 Ligand excluded by PLIP EDO.37: 7 residues within 4Å: Chain E: I.226, W.229, L.230, I.234, R.264, L.265, L.268 Ligand excluded by PLIP EDO.38: 7 residues within 4Å: Chain E: W.194, D.227, R.228, L.230, S.484, H.518, T.554 Ligand excluded by PLIP EDO.39: 7 residues within 4Å: Chain E: P.164, L.165, V.166, L.171, E.215, I.216, G.217 Ligand excluded by PLIP EDO.40: 4 residues within 4Å: Chain E: Y.543, C.544, T.545 Chain G: R.108 Ligand excluded by PLIP EDO.41: 5 residues within 4Å: Chain E: F.48, T.88, P.128, W.160, Q.271 Ligand excluded by PLIP EDO.42: 6 residues within 4Å: Chain E: E.475, Y.476, T.477, E.564, T.565, V.566 Ligand excluded by PLIP EDO.45: 7 residues within 4Å: Chain F: N.198, R.199, I.200, Q.213, I.214, G.215, C.216 Ligand excluded by PLIP EDO.49: 10 residues within 4Å: Chain G: L.119, G.122, A.123, L.127, A.129, F.130, H.149, S.157, M.158, F.159 Ligand excluded by PLIP EDO.50: 6 residues within 4Å: Chain A: F.54, Q.74, Q.117 Chain G: P.403, N.404, V.407 Ligand excluded by PLIP EDO.51: 6 residues within 4Å: Chain G: K.93, L.94, L.131, L.132, P.133, R.162 Ligand excluded by PLIP EDO.52: 7 residues within 4Å: Chain G: I.226, W.229, L.230, I.234, R.264, L.265, L.268 Ligand excluded by PLIP EDO.53: 7 residues within 4Å: Chain G: W.194, D.227, R.228, L.230, S.484, H.518, T.554 Ligand excluded by PLIP EDO.54: 7 residues within 4Å: Chain G: P.164, L.165, V.166, L.171, E.215, I.216, G.217 Ligand excluded by PLIP EDO.55: 4 residues within 4Å: Chain E: R.108 Chain G: Y.543, C.544, T.545 Ligand excluded by PLIP EDO.56: 5 residues within 4Å: Chain G: F.48, T.88, P.128, W.160, Q.271 Ligand excluded by PLIP EDO.57: 6 residues within 4Å: Chain G: E.475, Y.476, T.477, E.564, T.565, V.566 Ligand excluded by PLIP EDO.60: 7 residues within 4Å: Chain H: N.198, R.199, I.200, Q.213, I.214, G.215, C.216 Ligand excluded by PLIP

4 x GOL: GLYCEROL(Non-functional Binders)

GOL.13: 8 residues within 4Å: Chain A: E.137, D.138, N.139, T.140, N.199, L.203 Chain C: R.609, T.626 8 PLIP interactions: 2 interactions with chain C, 6 interactions with chain A Hydrogen bonds: C:R.609, A:E.137, A:E.137, A:N.139, A:T.140, A:N.199 Water bridges: C:T.626, A:N.139 GOL.28: 8 residues within 4Å: Chain A: R.609, T.626 Chain C: E.137, D.138, N.139, T.140, N.199, L.203 8 PLIP interactions: 6 interactions with chain C, 2 interactions with chain A Hydrogen bonds: C:E.137, C:E.137, C:N.139, C:T.140, C:N.199, A:R.609 Water bridges: C:N.139, A:T.626 GOL.43: 8 residues within 4Å: Chain E: E.137, D.138, N.139, T.140, N.199, L.203 Chain G: R.609, T.626 6 PLIP interactions: 4 interactions with chain E, 2 interactions with chain G Hydrogen bonds: E:E.137, E:N.139, E:N.199, G:R.609 Water bridges: E:N.139, G:T.626 GOL.58: 8 residues within 4Å: Chain E: R.609, T.626 Chain G: E.137, D.138, N.139, T.140, N.199, L.203 6 PLIP interactions: 4 interactions with chain G, 2 interactions with chain E Hydrogen bonds: G:E.137, G:N.139, G:N.199, E:R.609 Water bridges: G:N.139, E:T.626

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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