SMTL ID : 9n3n.1

Crystal structure of PRMT5:MEP50 in complex with MTA and oxamide compound 3

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.75 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 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, A:R.429 Water bridges: A:N.402 pi-Cation interactions: A:K.401 MTA.25: 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: 01.26 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, C:R.429 Water bridges: C:N.402 pi-Cation interactions: C:K.401 MTA.49: 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: 01.50 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, E:R.429 Water bridges: E:N.402 pi-Cation interactions: E:K.401 MTA.73: 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: 01.74 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, G:R.429 Water bridges: G:N.402 pi-Cation interactions: G:K.401

4 x 01: N-(6-amino-5-cyclopropylpyridin-3-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, S.447, E.452, V.511, 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:V.334, A:F.335, A:F.335, A:F.335, A:W.587, A:F.588 Hydrogen bonds: A:E.443, A:S.586, A:F.588 Water bridges: A:Q.317, A:S.447 01.26: 15 residues within 4Å: Chain C: Q.317, S.318, L.320, V.334, F.335, K.341, E.443, L.445, S.447, E.452, V.511, S.586, W.587, F.588 Ligands: MTA.25 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:F.335, C:W.587, C:F.588 Hydrogen bonds: C:E.443, C:S.586, C:F.588 Water bridges: C:Q.317, C:S.447 01.50: 15 residues within 4Å: Chain E: Q.317, S.318, L.320, V.334, F.335, K.341, E.443, L.445, S.447, E.452, V.511, S.586, W.587, F.588 Ligands: MTA.49 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:F.335, E:W.587, E:F.588 Hydrogen bonds: E:E.443, E:S.586, E:F.588 Water bridges: E:Q.317, E:S.447 01.74: 15 residues within 4Å: Chain G: Q.317, S.318, L.320, V.334, F.335, K.341, E.443, L.445, S.447, E.452, V.511, S.586, W.587, F.588 Ligands: MTA.73 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:F.335, G:W.587, G:F.588 Hydrogen bonds: G:E.443, G:S.586, G:F.588 Water bridges: G:Q.317, G:S.447

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

CL.3: 2 residues within 4Å: Chain A: Q.117 Chain G: P.403 Ligand excluded by PLIP CL.4: 3 residues within 4Å: Chain A: S.329 Chain G: G.83, W.86 Ligand excluded by PLIP CL.5: 4 residues within 4Å: Chain A: R.542, Y.543 Chain C: R.109, E.112 Ligand excluded by PLIP CL.6: 4 residues within 4Å: Chain A: Q.596, S.631, A.632, H.634 Ligand excluded by PLIP CL.27: 2 residues within 4Å: Chain C: Q.117 Chain E: P.403 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: 4 residues within 4Å: Chain A: R.109, E.112 Chain C: R.542, Y.543 Ligand excluded by PLIP CL.30: 4 residues within 4Å: Chain C: Q.596, S.631, A.632, H.634 Ligand excluded by PLIP CL.51: 2 residues within 4Å: Chain C: P.403 Chain E: Q.117 Ligand excluded by PLIP CL.52: 3 residues within 4Å: Chain C: G.83, W.86 Chain E: S.329 Ligand excluded by PLIP CL.53: 4 residues within 4Å: Chain E: R.542, Y.543 Chain G: R.109, E.112 Ligand excluded by PLIP CL.54: 4 residues within 4Å: Chain E: Q.596, S.631, A.632, H.634 Ligand excluded by PLIP CL.75: 2 residues within 4Å: Chain A: P.403 Chain G: Q.117 Ligand excluded by PLIP CL.76: 3 residues within 4Å: Chain A: G.83, W.86 Chain G: S.329 Ligand excluded by PLIP CL.77: 4 residues within 4Å: Chain E: R.109, E.112 Chain G: R.542, Y.543 Ligand excluded by PLIP CL.78: 4 residues within 4Å: Chain G: Q.596, S.631, A.632, H.634 Ligand excluded by PLIP

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

EDO.7: 6 residues within 4Å: Chain A: E.137, D.138, N.139, T.140, N.199, L.203 Ligand excluded by PLIP EDO.8: 5 residues within 4Å: Chain A: Y.187, H.224, D.227, E.551, V.552 Ligand excluded by PLIP EDO.9: 5 residues within 4Å: Chain A: K.401, S.425, S.426, D.427 Ligands: EDO.10 Ligand excluded by PLIP EDO.10: 4 residues within 4Å: Chain A: L.323, K.401, D.427 Ligands: EDO.9 Ligand excluded by PLIP EDO.11: 3 residues within 4Å: Chain A: F.517, H.518, Q.519 Ligand excluded by PLIP EDO.12: 3 residues within 4Å: Chain A: D.170, E.186, K.192 Ligand excluded by PLIP EDO.13: 4 residues within 4Å: Chain A: F.48, T.88, W.160, Q.271 Ligand excluded by PLIP EDO.14: 4 residues within 4Å: Chain A: H.151 Chain C: T.637, R.639 Ligands: PGE.21 Ligand excluded by PLIP EDO.15: 11 residues within 4Å: Chain A: L.119, G.122, A.123, L.127, P.128, A.129, F.130, H.149, S.157, M.158, F.159 Ligand excluded by PLIP EDO.16: 9 residues within 4Å: Chain A: W.194, D.227, R.228, L.230, E.232, S.484, H.518, L.520, T.554 Ligand excluded by PLIP EDO.17: 5 residues within 4Å: Chain A: D.27, R.162, E.215, I.238, T.275 Ligand excluded by PLIP EDO.18: 1 residues within 4Å: Chain C: D.501 Ligand excluded by PLIP EDO.22: 5 residues within 4Å: Chain A: N.278, S.281 Chain B: K.129, Y.130, E.131 Ligand excluded by PLIP EDO.23: 4 residues within 4Å: Chain B: D.93, S.137, T.138, C.180 Ligand excluded by PLIP EDO.31: 6 residues within 4Å: Chain C: E.137, D.138, N.139, T.140, N.199, L.203 Ligand excluded by PLIP EDO.32: 5 residues within 4Å: Chain C: Y.187, H.224, D.227, E.551, V.552 Ligand excluded by PLIP EDO.33: 5 residues within 4Å: Chain C: K.401, S.425, S.426, D.427 Ligands: EDO.34 Ligand excluded by PLIP EDO.34: 4 residues within 4Å: Chain C: L.323, K.401, D.427 Ligands: EDO.33 Ligand excluded by PLIP EDO.35: 3 residues within 4Å: Chain C: F.517, H.518, Q.519 Ligand excluded by PLIP EDO.36: 3 residues within 4Å: Chain C: D.170, E.186, K.192 Ligand excluded by PLIP EDO.37: 4 residues within 4Å: Chain C: F.48, T.88, W.160, Q.271 Ligand excluded by PLIP EDO.38: 4 residues within 4Å: Chain A: T.637, R.639 Chain C: H.151 Ligands: PGE.45 Ligand excluded by PLIP EDO.39: 11 residues within 4Å: Chain C: L.119, G.122, A.123, L.127, P.128, A.129, F.130, H.149, S.157, M.158, F.159 Ligand excluded by PLIP EDO.40: 9 residues within 4Å: Chain C: W.194, D.227, R.228, L.230, E.232, S.484, H.518, L.520, T.554 Ligand excluded by PLIP EDO.41: 5 residues within 4Å: Chain C: D.27, R.162, E.215, I.238, T.275 Ligand excluded by PLIP EDO.42: 1 residues within 4Å: Chain A: D.501 Ligand excluded by PLIP EDO.46: 5 residues within 4Å: Chain C: N.278, S.281 Chain D: K.129, Y.130, E.131 Ligand excluded by PLIP EDO.47: 4 residues within 4Å: Chain D: D.93, S.137, T.138, C.180 Ligand excluded by PLIP EDO.55: 6 residues within 4Å: Chain E: E.137, D.138, N.139, T.140, N.199, L.203 Ligand excluded by PLIP EDO.56: 5 residues within 4Å: Chain E: Y.187, H.224, D.227, E.551, V.552 Ligand excluded by PLIP EDO.57: 5 residues within 4Å: Chain E: K.401, S.425, S.426, D.427 Ligands: EDO.58 Ligand excluded by PLIP EDO.58: 4 residues within 4Å: Chain E: L.323, K.401, D.427 Ligands: EDO.57 Ligand excluded by PLIP EDO.59: 3 residues within 4Å: Chain E: F.517, H.518, Q.519 Ligand excluded by PLIP EDO.60: 3 residues within 4Å: Chain E: D.170, E.186, K.192 Ligand excluded by PLIP EDO.61: 4 residues within 4Å: Chain E: F.48, T.88, W.160, Q.271 Ligand excluded by PLIP EDO.62: 4 residues within 4Å: Chain E: H.151 Chain G: T.637, R.639 Ligands: PGE.69 Ligand excluded by PLIP EDO.63: 11 residues within 4Å: Chain E: L.119, G.122, A.123, L.127, P.128, A.129, F.130, H.149, S.157, M.158, F.159 Ligand excluded by PLIP EDO.64: 9 residues within 4Å: Chain E: W.194, D.227, R.228, L.230, E.232, S.484, H.518, L.520, T.554 Ligand excluded by PLIP EDO.65: 5 residues within 4Å: Chain E: D.27, R.162, E.215, I.238, T.275 Ligand excluded by PLIP EDO.66: 1 residues within 4Å: Chain G: D.501 Ligand excluded by PLIP EDO.70: 5 residues within 4Å: Chain E: N.278, S.281 Chain F: K.129, Y.130, E.131 Ligand excluded by PLIP EDO.71: 4 residues within 4Å: Chain F: D.93, S.137, T.138, C.180 Ligand excluded by PLIP EDO.79: 6 residues within 4Å: Chain G: E.137, D.138, N.139, T.140, N.199, L.203 Ligand excluded by PLIP EDO.80: 5 residues within 4Å: Chain G: Y.187, H.224, D.227, E.551, V.552 Ligand excluded by PLIP EDO.81: 5 residues within 4Å: Chain G: K.401, S.425, S.426, D.427 Ligands: EDO.82 Ligand excluded by PLIP EDO.82: 4 residues within 4Å: Chain G: L.323, K.401, D.427 Ligands: EDO.81 Ligand excluded by PLIP EDO.83: 3 residues within 4Å: Chain G: F.517, H.518, Q.519 Ligand excluded by PLIP EDO.84: 3 residues within 4Å: Chain G: D.170, E.186, K.192 Ligand excluded by PLIP EDO.85: 4 residues within 4Å: Chain G: F.48, T.88, W.160, Q.271 Ligand excluded by PLIP EDO.86: 4 residues within 4Å: Chain E: T.637, R.639 Chain G: H.151 Ligands: PGE.93 Ligand excluded by PLIP EDO.87: 11 residues within 4Å: Chain G: L.119, G.122, A.123, L.127, P.128, A.129, F.130, H.149, S.157, M.158, F.159 Ligand excluded by PLIP EDO.88: 9 residues within 4Å: Chain G: W.194, D.227, R.228, L.230, E.232, S.484, H.518, L.520, T.554 Ligand excluded by PLIP EDO.89: 5 residues within 4Å: Chain G: D.27, R.162, E.215, I.238, T.275 Ligand excluded by PLIP EDO.90: 1 residues within 4Å: Chain E: D.501 Ligand excluded by PLIP EDO.94: 5 residues within 4Å: Chain G: N.278, S.281 Chain H: K.129, Y.130, E.131 Ligand excluded by PLIP EDO.95: 4 residues within 4Å: Chain H: D.93, S.137, T.138, C.180 Ligand excluded by PLIP

12 x PEG: DI(HYDROXYETHYL)ETHER(Non-functional Binders)

PEG.19: 7 residues within 4Å: Chain A: P.233, K.235, L.268, E.269, K.487, H.515, N.516 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:K.235, A:E.269, A:H.515, A:N.516 PEG.20: 3 residues within 4Å: Chain A: N.178, A.179, P.180 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.178, A:P.180 PEG.24: 9 residues within 4Å: Chain B: N.198, R.199, I.200, Q.213, G.215, C.216, G.220, Y.221, F.238 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:I.200, B:I.200, B:Q.213, B:C.216, B:Y.221 PEG.43: 7 residues within 4Å: Chain C: P.233, K.235, L.268, E.269, K.487, H.515, N.516 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:K.235, C:E.269, C:H.515, C:N.516 PEG.44: 3 residues within 4Å: Chain C: N.178, A.179, P.180 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:N.178, C:P.180 PEG.48: 9 residues within 4Å: Chain D: N.198, R.199, I.200, Q.213, G.215, C.216, G.220, Y.221, F.238 5 PLIP interactions: 5 interactions with chain D Hydrogen bonds: D:I.200, D:I.200, D:Q.213, D:C.216, D:Y.221 PEG.67: 7 residues within 4Å: Chain E: P.233, K.235, L.268, E.269, K.487, H.515, N.516 3 PLIP interactions: 3 interactions with chain E Hydrogen bonds: E:K.235, E:E.269, E:N.516 PEG.68: 3 residues within 4Å: Chain E: N.178, A.179, P.180 2 PLIP interactions: 2 interactions with chain E Hydrogen bonds: E:N.178, E:P.180 PEG.72: 9 residues within 4Å: Chain F: N.198, R.199, I.200, Q.213, G.215, C.216, G.220, Y.221, F.238 5 PLIP interactions: 5 interactions with chain F Hydrogen bonds: F:I.200, F:I.200, F:Q.213, F:C.216, F:Y.221 PEG.91: 7 residues within 4Å: Chain G: P.233, K.235, L.268, E.269, K.487, H.515, N.516 3 PLIP interactions: 3 interactions with chain G Hydrogen bonds: G:K.235, G:E.269, G:N.516 PEG.92: 3 residues within 4Å: Chain G: N.178, A.179, P.180 2 PLIP interactions: 2 interactions with chain G Hydrogen bonds: G:N.178, G:P.180 PEG.96: 9 residues within 4Å: Chain H: N.198, R.199, I.200, Q.213, G.215, C.216, G.220, Y.221, F.238 5 PLIP interactions: 5 interactions with chain H Hydrogen bonds: H:I.200, H:I.200, H:Q.213, H:C.216, H:Y.221

4 x PGE: TRIETHYLENE GLYCOL(Non-functional Binders)

PGE.21: 7 residues within 4Å: Chain A: I.150, H.151, S.207, K.208, R.209, R.493 Ligands: EDO.14 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Y.206, A:K.208 PGE.45: 7 residues within 4Å: Chain C: I.150, H.151, S.207, K.208, R.209, R.493 Ligands: EDO.38 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:Y.206, C:K.208 PGE.69: 7 residues within 4Å: Chain E: I.150, H.151, S.207, K.208, R.209, R.493 Ligands: EDO.62 2 PLIP interactions: 2 interactions with chain E Hydrogen bonds: E:Y.206, E:K.208 PGE.93: 7 residues within 4Å: Chain G: I.150, H.151, S.207, K.208, R.209, R.493 Ligands: EDO.86 2 PLIP interactions: 2 interactions with chain G Hydrogen bonds: G:Y.206, G:K.208

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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