SMTL ID : 9mgr.1

Crystal structure of PRMT5:MEP50 in complex with MTA and compound 51

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.07 Å

Oligo State

hetero-4-4-mer

Ligands

4 x 01: 6-[(1-acetylazetidin-3-yl)amino]-N-[(2R)-2-hydroxy-2-{(3S)-7-[(4-methyl-1,3-oxazol-5-yl)methoxy]-1,2,3,4-tetrahydroisoquinolin-3-yl}ethyl]-2-(4-methylpiperidin-1-yl)pyrimidine-4-carboxamide

01.1: 26 residues within 4Å: Chain A: F.308, Y.312, Q.317, L.327, Y.332, V.334, F.335, E.336, K.341, Y.342, G.373, A.374, G.375, R.376, P.378, E.443, G.446, S.447, E.452, V.511, F.585, S.586, W.587, F.588 Ligands: MTA.2, EDO.4 17 PLIP interactions: 17 interactions with chain A Hydrophobic interactions: A:L.327, A:V.334, A:F.335, A:P.378, A:F.585, A:F.588 Hydrogen bonds: A:R.376, A:G.377, A:S.447, A:S.447, A:F.585, A:W.587, A:F.588 Water bridges: A:S.447, A:E.452 pi-Stacking: A:F.335, A:F.335 01.18: 26 residues within 4Å: Chain C: F.308, Y.312, Q.317, L.327, Y.332, V.334, F.335, E.336, K.341, Y.342, G.373, A.374, G.375, R.376, P.378, E.443, G.446, S.447, E.452, V.511, F.585, S.586, W.587, F.588 Ligands: MTA.19, EDO.21 17 PLIP interactions: 17 interactions with chain C Hydrophobic interactions: C:L.327, C:V.334, C:F.335, C:P.378, C:F.585, C:F.588 Hydrogen bonds: C:R.376, C:G.377, C:S.447, C:S.447, C:F.585, C:W.587, C:F.588 Water bridges: C:S.447, C:E.452 pi-Stacking: C:F.335, C:F.335 01.35: 26 residues within 4Å: Chain E: F.308, Y.312, Q.317, L.327, Y.332, V.334, F.335, E.336, K.341, Y.342, G.373, A.374, G.375, R.376, P.378, E.443, G.446, S.447, E.452, V.511, F.585, S.586, W.587, F.588 Ligands: MTA.36, EDO.38 17 PLIP interactions: 17 interactions with chain E Hydrophobic interactions: E:L.327, E:V.334, E:F.335, E:P.378, E:F.585, E:F.588 Hydrogen bonds: E:R.376, E:G.377, E:S.447, E:S.447, E:F.585, E:W.587, E:F.588 Water bridges: E:S.447, E:E.452 pi-Stacking: E:F.335, E:F.335 01.52: 26 residues within 4Å: Chain G: F.308, Y.312, Q.317, L.327, Y.332, V.334, F.335, E.336, K.341, Y.342, G.373, A.374, G.375, R.376, P.378, E.443, G.446, S.447, E.452, V.511, F.585, S.586, W.587, F.588 Ligands: MTA.53, EDO.55 17 PLIP interactions: 17 interactions with chain G Hydrophobic interactions: G:L.327, G:V.334, G:F.335, G:P.378, G:F.585, G:F.588 Hydrogen bonds: G:R.376, G:G.377, G:S.447, G:S.447, G:F.585, G:W.587, G:F.588 Water bridges: G:S.447, G:E.452 pi-Stacking: G:F.335, G:F.335

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

MTA.2: 17 residues within 4Å: Chain A: L.323, L.327, 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: 01.1, EDO.4 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.19: 17 residues within 4Å: Chain C: L.323, L.327, 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: 01.18, EDO.21 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.36: 17 residues within 4Å: Chain E: L.323, L.327, 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: 01.35, EDO.38 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.53: 17 residues within 4Å: Chain G: L.323, L.327, 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: 01.52, EDO.55 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

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

EDO.3: 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.4: 7 residues within 4Å: Chain A: K.341, E.443, L.445, E.452, W.587 Ligands: 01.1, MTA.2 Ligand excluded by PLIP EDO.5: 8 residues within 4Å: Chain A: W.194, D.227, R.228, L.230, S.484, H.518, T.554 Ligands: EDO.6 Ligand excluded by PLIP EDO.6: 9 residues within 4Å: Chain A: Y.187, E.191, H.224, D.227, R.228, H.518, V.552, N.553 Ligands: EDO.5 Ligand excluded by PLIP EDO.7: 4 residues within 4Å: Chain A: L.316, Q.317, S.318, C.495 Ligand excluded by PLIP EDO.8: 5 residues within 4Å: Chain A: R.109, E.112 Chain C: N.541, R.542, Y.543 Ligand excluded by PLIP EDO.9: 5 residues within 4Å: Chain A: L.323, K.401, D.427, R.429, L.645 Ligand excluded by PLIP EDO.10: 3 residues within 4Å: Chain A: Y.543, C.544, T.545 Ligand excluded by PLIP EDO.11: 3 residues within 4Å: Chain A: P.523, Q.524, P.525 Ligand excluded by PLIP EDO.12: 7 residues within 4Å: Chain A: F.54, Q.74, Q.117, F.121 Chain G: P.403, N.404, V.407 Ligand excluded by PLIP EDO.13: 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.14: 4 residues within 4Å: Chain A: I.150, S.207, K.208, R.209 Ligand excluded by PLIP EDO.15: 5 residues within 4Å: Chain A: I.234, L.268, K.487, H.515, N.516 Ligand excluded by PLIP EDO.16: 6 residues within 4Å: Chain A: L.307, F.308, A.309, K.310, G.311, Y.312 Ligand excluded by PLIP EDO.17: 5 residues within 4Å: Chain B: N.198, G.220, Y.221, P.223, F.238 Ligand excluded by PLIP EDO.20: 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.21: 7 residues within 4Å: Chain C: K.341, E.443, L.445, E.452, W.587 Ligands: 01.18, MTA.19 Ligand excluded by PLIP EDO.22: 8 residues within 4Å: Chain C: W.194, D.227, R.228, L.230, S.484, H.518, T.554 Ligands: EDO.23 Ligand excluded by PLIP EDO.23: 9 residues within 4Å: Chain C: Y.187, E.191, H.224, D.227, R.228, H.518, V.552, N.553 Ligands: EDO.22 Ligand excluded by PLIP EDO.24: 4 residues within 4Å: Chain C: L.316, Q.317, S.318, C.495 Ligand excluded by PLIP EDO.25: 5 residues within 4Å: Chain A: N.541, R.542, Y.543 Chain C: R.109, E.112 Ligand excluded by PLIP EDO.26: 5 residues within 4Å: Chain C: L.323, K.401, D.427, R.429, L.645 Ligand excluded by PLIP EDO.27: 3 residues within 4Å: Chain C: Y.543, C.544, T.545 Ligand excluded by PLIP EDO.28: 3 residues within 4Å: Chain C: P.523, Q.524, P.525 Ligand excluded by PLIP EDO.29: 7 residues within 4Å: Chain C: F.54, Q.74, Q.117, F.121 Chain E: P.403, N.404, V.407 Ligand excluded by PLIP EDO.30: 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.31: 4 residues within 4Å: Chain C: I.150, S.207, K.208, R.209 Ligand excluded by PLIP EDO.32: 5 residues within 4Å: Chain C: I.234, L.268, K.487, H.515, N.516 Ligand excluded by PLIP EDO.33: 6 residues within 4Å: Chain C: L.307, F.308, A.309, K.310, G.311, Y.312 Ligand excluded by PLIP EDO.34: 5 residues within 4Å: Chain D: N.198, G.220, Y.221, P.223, F.238 Ligand excluded by PLIP EDO.37: 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.38: 7 residues within 4Å: Chain E: K.341, E.443, L.445, E.452, W.587 Ligands: 01.35, MTA.36 Ligand excluded by PLIP EDO.39: 8 residues within 4Å: Chain E: W.194, D.227, R.228, L.230, S.484, H.518, T.554 Ligands: EDO.40 Ligand excluded by PLIP EDO.40: 9 residues within 4Å: Chain E: Y.187, E.191, H.224, D.227, R.228, H.518, V.552, N.553 Ligands: EDO.39 Ligand excluded by PLIP EDO.41: 4 residues within 4Å: Chain E: L.316, Q.317, S.318, C.495 Ligand excluded by PLIP EDO.42: 5 residues within 4Å: Chain E: R.109, E.112 Chain G: N.541, R.542, Y.543 Ligand excluded by PLIP EDO.43: 5 residues within 4Å: Chain E: L.323, K.401, D.427, R.429, L.645 Ligand excluded by PLIP EDO.44: 3 residues within 4Å: Chain E: Y.543, C.544, T.545 Ligand excluded by PLIP EDO.45: 3 residues within 4Å: Chain E: P.523, Q.524, P.525 Ligand excluded by PLIP EDO.46: 7 residues within 4Å: Chain C: P.403, N.404, V.407 Chain E: F.54, Q.74, Q.117, F.121 Ligand excluded by PLIP EDO.47: 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.48: 4 residues within 4Å: Chain E: I.150, S.207, K.208, R.209 Ligand excluded by PLIP EDO.49: 5 residues within 4Å: Chain E: I.234, L.268, K.487, H.515, N.516 Ligand excluded by PLIP EDO.50: 6 residues within 4Å: Chain E: L.307, F.308, A.309, K.310, G.311, Y.312 Ligand excluded by PLIP EDO.51: 5 residues within 4Å: Chain F: N.198, G.220, Y.221, P.223, F.238 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: 7 residues within 4Å: Chain G: K.341, E.443, L.445, E.452, W.587 Ligands: 01.52, MTA.53 Ligand excluded by PLIP EDO.56: 8 residues within 4Å: Chain G: W.194, D.227, R.228, L.230, S.484, H.518, T.554 Ligands: EDO.57 Ligand excluded by PLIP EDO.57: 9 residues within 4Å: Chain G: Y.187, E.191, H.224, D.227, R.228, H.518, V.552, N.553 Ligands: EDO.56 Ligand excluded by PLIP EDO.58: 4 residues within 4Å: Chain G: L.316, Q.317, S.318, C.495 Ligand excluded by PLIP EDO.59: 5 residues within 4Å: Chain E: N.541, R.542, Y.543 Chain G: R.109, E.112 Ligand excluded by PLIP EDO.60: 5 residues within 4Å: Chain G: L.323, K.401, D.427, R.429, L.645 Ligand excluded by PLIP EDO.61: 3 residues within 4Å: Chain G: Y.543, C.544, T.545 Ligand excluded by PLIP EDO.62: 3 residues within 4Å: Chain G: P.523, Q.524, P.525 Ligand excluded by PLIP EDO.63: 7 residues within 4Å: Chain A: P.403, N.404, V.407 Chain G: F.54, Q.74, Q.117, F.121 Ligand excluded by PLIP EDO.64: 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.65: 4 residues within 4Å: Chain G: I.150, S.207, K.208, R.209 Ligand excluded by PLIP EDO.66: 5 residues within 4Å: Chain G: I.234, L.268, K.487, H.515, N.516 Ligand excluded by PLIP EDO.67: 6 residues within 4Å: Chain G: L.307, F.308, A.309, K.310, G.311, Y.312 Ligand excluded by PLIP EDO.68: 5 residues within 4Å: Chain H: N.198, G.220, Y.221, P.223, F.238 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Cottrell, K.M. et al., MTA-Cooperative PRMT5 Inhibitors: Mechanism Switching Through Structure-Based Design. J.Med.Chem. (2025)

Release Date

2025-03-05

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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