SMTL ID : 9mgl.1

Crystal structure of PRMT5:MEP50 in complex with MTA and GSK3326595

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.25 Å

Oligo State

hetero-4-4-mer

Ligands

4 x 01: pemrametostat

01.1: 25 residues within 4Å: Chain A: F.308, A.309, Y.312, Q.317, L.320, L.327, T.331, Y.332, V.334, F.335, E.336, K.337, K.341, Y.342, E.443, L.445, G.446, S.447, E.452, V.511, F.585, S.586, W.587, F.588 Ligands: MTA.2 19 PLIP interactions: 19 interactions with chain A Hydrophobic interactions: A:Y.312, A:L.327, A:F.335, A:F.335, A:F.585, A:F.585, A:F.588, A:F.588 Hydrogen bonds: A:Q.317, A:L.445, A:F.585, A:W.587, A:F.588 Water bridges: A:Y.312, A:L.320, A:S.447 Salt bridges: A:E.452 pi-Stacking: A:F.335 pi-Cation interactions: A:F.335 01.17: 25 residues within 4Å: Chain C: F.308, A.309, Y.312, Q.317, L.320, L.327, T.331, Y.332, V.334, F.335, E.336, K.337, K.341, Y.342, E.443, L.445, G.446, S.447, E.452, V.511, F.585, S.586, W.587, F.588 Ligands: MTA.18 19 PLIP interactions: 19 interactions with chain C Hydrophobic interactions: C:Y.312, C:L.327, C:F.335, C:F.335, C:F.585, C:F.585, C:F.588, C:F.588 Hydrogen bonds: C:Q.317, C:L.445, C:F.585, C:W.587, C:F.588 Water bridges: C:Y.312, C:L.320, C:S.447 Salt bridges: C:E.452 pi-Stacking: C:F.335 pi-Cation interactions: C:F.335 01.33: 25 residues within 4Å: Chain E: F.308, A.309, Y.312, Q.317, L.320, L.327, T.331, Y.332, V.334, F.335, E.336, K.337, K.341, Y.342, E.443, L.445, G.446, S.447, E.452, V.511, F.585, S.586, W.587, F.588 Ligands: MTA.34 19 PLIP interactions: 19 interactions with chain E Hydrophobic interactions: E:Y.312, E:L.327, E:F.335, E:F.335, E:F.585, E:F.585, E:F.588, E:F.588 Hydrogen bonds: E:Q.317, E:L.445, E:F.585, E:W.587, E:F.588 Water bridges: E:Y.312, E:L.320, E:E.452 Salt bridges: E:E.452 pi-Stacking: E:F.335 pi-Cation interactions: E:F.335 01.49: 25 residues within 4Å: Chain G: F.308, A.309, Y.312, Q.317, L.320, L.327, T.331, Y.332, V.334, F.335, E.336, K.337, K.341, Y.342, E.443, L.445, G.446, S.447, E.452, V.511, F.585, S.586, W.587, F.588 Ligands: MTA.50 19 PLIP interactions: 19 interactions with chain G Hydrophobic interactions: G:Y.312, G:L.327, G:F.335, G:F.335, G:F.585, G:F.585, G:F.588, G:F.588 Hydrogen bonds: G:Q.317, G:L.445, G:F.585, G:W.587, G:F.588 Water bridges: G:Y.312, G:L.320, G:E.452 Salt bridges: G:E.452 pi-Stacking: G:F.335 pi-Cation interactions: G:F.335

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

MTA.2: 18 residues within 4Å: Chain A: P.322, L.323, L.327, Y.332, G.373, G.375, V.399, E.400, K.401, N.402, S.426, D.427, M.428, R.429, E.443, L.444, C.457 Ligands: 01.1 8 PLIP interactions: 8 interactions with chain A Hydrogen bonds: A:P.322, A:Y.332, A:Y.332, A:G.375, A:K.401, A:D.427, A:M.428, A:R.429 MTA.18: 18 residues within 4Å: Chain C: P.322, L.323, L.327, Y.332, G.373, G.375, V.399, E.400, K.401, N.402, S.426, D.427, M.428, R.429, E.443, L.444, C.457 Ligands: 01.17 8 PLIP interactions: 8 interactions with chain C Hydrogen bonds: C:P.322, C:Y.332, C:Y.332, C:G.375, C:K.401, C:D.427, C:M.428, C:R.429 MTA.34: 18 residues within 4Å: Chain E: P.322, L.323, L.327, Y.332, G.373, G.375, V.399, E.400, K.401, N.402, S.426, D.427, M.428, R.429, E.443, L.444, C.457 Ligands: 01.33 8 PLIP interactions: 8 interactions with chain E Hydrogen bonds: E:P.322, E:Y.332, E:Y.332, E:G.375, E:K.401, E:D.427, E:M.428, E:R.429 MTA.50: 18 residues within 4Å: Chain G: P.322, L.323, L.327, Y.332, G.373, G.375, V.399, E.400, K.401, N.402, S.426, D.427, M.428, R.429, E.443, L.444, C.457 Ligands: 01.49 8 PLIP interactions: 8 interactions with chain G Hydrogen bonds: G:P.322, G:Y.332, G:Y.332, G:G.375, G:K.401, G:D.427, G:M.428, G:R.429

12 x SO4: SULFATE ION(Non-functional Binders)

SO4.3: 5 residues within 4Å: Chain A: F.48, V.91, P.128, W.160, Q.271 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Q.271 SO4.4: 2 residues within 4Å: Chain A: N.223, R.260 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:R.260 SO4.5: 5 residues within 4Å: Chain A: Y.206, S.207, K.208, N.490, R.493 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:K.208, A:R.493 Water bridges: A:H.151 Salt bridges: A:K.208 SO4.19: 5 residues within 4Å: Chain C: F.48, V.91, P.128, W.160, Q.271 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:Q.271 SO4.20: 2 residues within 4Å: Chain C: N.223, R.260 1 PLIP interactions: 1 interactions with chain C Salt bridges: C:R.260 SO4.21: 5 residues within 4Å: Chain C: Y.206, S.207, K.208, N.490, R.493 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:K.208, C:R.493 Water bridges: C:H.151 Salt bridges: C:K.208 SO4.35: 5 residues within 4Å: Chain E: F.48, V.91, P.128, W.160, Q.271 1 PLIP interactions: 1 interactions with chain E Hydrogen bonds: E:Q.271 SO4.36: 2 residues within 4Å: Chain E: N.223, R.260 1 PLIP interactions: 1 interactions with chain E Salt bridges: E:R.260 SO4.37: 5 residues within 4Å: Chain E: Y.206, S.207, K.208, N.490, R.493 4 PLIP interactions: 4 interactions with chain E Hydrogen bonds: E:K.208, E:R.493 Water bridges: E:H.151 Salt bridges: E:K.208 SO4.51: 5 residues within 4Å: Chain G: F.48, V.91, P.128, W.160, Q.271 1 PLIP interactions: 1 interactions with chain G Hydrogen bonds: G:Q.271 SO4.52: 2 residues within 4Å: Chain G: N.223, R.260 1 PLIP interactions: 1 interactions with chain G Salt bridges: G:R.260 SO4.53: 5 residues within 4Å: Chain G: Y.206, S.207, K.208, N.490, R.493 4 PLIP interactions: 4 interactions with chain G Hydrogen bonds: G:K.208, G:R.493 Water bridges: G:H.151 Salt bridges: G:K.208

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

EDO.6: 4 residues within 4Å: Chain A: Y.543, C.544, T.545 Chain C: R.108 Ligand excluded by PLIP EDO.7: 11 residues within 4Å: Chain A: S.329, Q.330, E.333, R.376 Chain G: D.78, L.79, L.81, S.82, G.83, W.86, L.125 Ligand excluded by PLIP EDO.8: 1 residues within 4Å: Chain A: H.154 Ligand excluded by PLIP EDO.9: 4 residues within 4Å: Chain A: K.43, Q.44, G.45, L.289 Ligand excluded by PLIP EDO.10: 6 residues within 4Å: Chain A: K.103, V.104, E.105, R.108 Chain B: Y.221, N.242 Ligand excluded by PLIP EDO.11: 8 residues within 4Å: Chain A: N.120, A.123, Y.124, H.155 Chain G: N.326, L.327, E.328, N.404 Ligand excluded by PLIP EDO.12: 8 residues within 4Å: Chain A: I.594, K.595, Q.596, I.598, S.631, A.632, H.634 Chain C: Q.596 Ligand excluded by PLIP EDO.14: 6 residues within 4Å: Chain A: R.162 Chain B: D.133, D.134, K.153, D.154, I.155 Ligand excluded by PLIP EDO.15: 5 residues within 4Å: Chain B: R.300, S.301, Q.302, A.303 Ligands: EDO.16 Ligand excluded by PLIP EDO.16: 7 residues within 4Å: Chain B: F.299, R.300, S.301, A.303, V.331, H.333 Ligands: EDO.15 Ligand excluded by PLIP EDO.22: 4 residues within 4Å: Chain A: R.108 Chain C: Y.543, C.544, T.545 Ligand excluded by PLIP EDO.23: 11 residues within 4Å: Chain C: S.329, Q.330, E.333, R.376 Chain E: D.78, L.79, L.81, S.82, G.83, W.86, L.125 Ligand excluded by PLIP EDO.24: 1 residues within 4Å: Chain C: H.154 Ligand excluded by PLIP EDO.25: 4 residues within 4Å: Chain C: K.43, Q.44, G.45, L.289 Ligand excluded by PLIP EDO.26: 6 residues within 4Å: Chain C: K.103, V.104, E.105, R.108 Chain D: Y.221, N.242 Ligand excluded by PLIP EDO.27: 8 residues within 4Å: Chain C: N.120, A.123, Y.124, H.155 Chain E: N.326, L.327, E.328, N.404 Ligand excluded by PLIP EDO.28: 8 residues within 4Å: Chain A: Q.596 Chain C: I.594, K.595, Q.596, I.598, S.631, A.632, H.634 Ligand excluded by PLIP EDO.30: 6 residues within 4Å: Chain C: R.162 Chain D: D.133, D.134, K.153, D.154, I.155 Ligand excluded by PLIP EDO.31: 5 residues within 4Å: Chain D: R.300, S.301, Q.302, A.303 Ligands: EDO.32 Ligand excluded by PLIP EDO.32: 7 residues within 4Å: Chain D: F.299, R.300, S.301, A.303, V.331, H.333 Ligands: EDO.31 Ligand excluded by PLIP EDO.38: 4 residues within 4Å: Chain E: Y.543, C.544, T.545 Chain G: R.108 Ligand excluded by PLIP EDO.39: 11 residues within 4Å: Chain C: D.78, L.79, L.81, S.82, G.83, W.86, L.125 Chain E: S.329, Q.330, E.333, R.376 Ligand excluded by PLIP EDO.40: 1 residues within 4Å: Chain E: H.154 Ligand excluded by PLIP EDO.41: 4 residues within 4Å: Chain E: K.43, Q.44, G.45, L.289 Ligand excluded by PLIP EDO.42: 6 residues within 4Å: Chain E: K.103, V.104, E.105, R.108 Chain F: Y.221, N.242 Ligand excluded by PLIP EDO.43: 8 residues within 4Å: Chain C: N.326, L.327, E.328, N.404 Chain E: N.120, A.123, Y.124, H.155 Ligand excluded by PLIP EDO.44: 8 residues within 4Å: Chain E: I.594, K.595, Q.596, I.598, S.631, A.632, H.634 Chain G: Q.596 Ligand excluded by PLIP EDO.46: 6 residues within 4Å: Chain E: R.162 Chain F: D.133, D.134, K.153, D.154, I.155 Ligand excluded by PLIP EDO.47: 5 residues within 4Å: Chain F: R.300, S.301, Q.302, A.303 Ligands: EDO.48 Ligand excluded by PLIP EDO.48: 7 residues within 4Å: Chain F: F.299, R.300, S.301, A.303, V.331, H.333 Ligands: EDO.47 Ligand excluded by PLIP EDO.54: 4 residues within 4Å: Chain E: R.108 Chain G: Y.543, C.544, T.545 Ligand excluded by PLIP EDO.55: 11 residues within 4Å: Chain A: D.78, L.79, L.81, S.82, G.83, W.86, L.125 Chain G: S.329, Q.330, E.333, R.376 Ligand excluded by PLIP EDO.56: 1 residues within 4Å: Chain G: H.154 Ligand excluded by PLIP EDO.57: 4 residues within 4Å: Chain G: K.43, Q.44, G.45, L.289 Ligand excluded by PLIP EDO.58: 6 residues within 4Å: Chain G: K.103, V.104, E.105, R.108 Chain H: Y.221, N.242 Ligand excluded by PLIP EDO.59: 8 residues within 4Å: Chain A: N.326, L.327, E.328, N.404 Chain G: N.120, A.123, Y.124, H.155 Ligand excluded by PLIP EDO.60: 8 residues within 4Å: Chain E: Q.596 Chain G: I.594, K.595, Q.596, I.598, S.631, A.632, H.634 Ligand excluded by PLIP EDO.62: 6 residues within 4Å: Chain G: R.162 Chain H: D.133, D.134, K.153, D.154, I.155 Ligand excluded by PLIP EDO.63: 5 residues within 4Å: Chain H: R.300, S.301, Q.302, A.303 Ligands: EDO.64 Ligand excluded by PLIP EDO.64: 7 residues within 4Å: Chain H: F.299, R.300, S.301, A.303, V.331, H.333 Ligands: EDO.63 Ligand excluded by PLIP

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

PEG.13: 5 residues within 4Å: Chain A: F.414, E.416, W.417, G.418, S.419 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:S.419 PEG.29: 5 residues within 4Å: Chain C: F.414, E.416, W.417, G.418, S.419 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:S.419 PEG.45: 5 residues within 4Å: Chain E: F.414, E.416, W.417, G.418, S.419 1 PLIP interactions: 1 interactions with chain E Hydrogen bonds: E:S.419 PEG.61: 5 residues within 4Å: Chain G: F.414, E.416, W.417, G.418, S.419 1 PLIP interactions: 1 interactions with chain G Hydrogen bonds: G:S.419

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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