SMTL ID : 9mgp.1

Crystal structure of PRMT5:MEP50 in complex with MTA and compound 46a

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.67 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, 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 7 PLIP interactions: 7 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 MTA.25: 16 residues within 4Å: Chain C: P.322, L.323, 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: 01.26 7 PLIP interactions: 7 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 MTA.49: 16 residues within 4Å: Chain E: P.322, L.323, 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: 01.50 6 PLIP interactions: 6 interactions with chain E Hydrogen bonds: E:Y.332, E:G.375, E:K.401, E:D.427, E:M.428, E:R.429 MTA.73: 16 residues within 4Å: Chain G: P.322, L.323, 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: 01.74 6 PLIP interactions: 6 interactions with chain G Hydrogen bonds: G:Y.332, G:G.375, G:K.401, G:D.427, G:M.428, G:R.429

4 x 01: [2-(cyclobutylamino)pyridin-4-yl][(3R,4R)-3-hydroxy-4-{6-[(1-methyl-1H-pyrazol-5-yl)methyl]-3,4-dihydroisoquinolin-2(1H)-yl}piperidin-1-yl]methanone

01.2: 25 residues within 4Å: Chain A: F.308, Y.312, Q.317, L.320, L.327, Y.332, F.335, E.336, K.341, Y.342, A.374, G.375, R.376, P.378, E.443, L.445, G.446, S.447, 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:Y.312, A:L.320, A:L.327, A:F.335, A:F.335, A:F.335, A:F.335, A:P.378, A:V.511, A:F.585, A:F.588 Hydrogen bonds: A:R.376, A:F.585, A:W.587, A:F.588 Salt bridges: A:E.452 pi-Cation interactions: A:F.335 01.26: 25 residues within 4Å: Chain C: F.308, Y.312, Q.317, L.320, L.327, Y.332, F.335, E.336, K.341, Y.342, A.374, G.375, R.376, P.378, E.443, L.445, G.446, S.447, E.452, V.511, F.585, S.586, W.587, F.588 Ligands: MTA.25 17 PLIP interactions: 17 interactions with chain C Hydrophobic interactions: C:Y.312, C:L.320, C:L.327, C:F.335, C:F.335, C:F.335, C:F.335, C:P.378, C:V.511, C:F.585, C:F.588 Hydrogen bonds: C:R.376, C:F.585, C:W.587, C:F.588 Salt bridges: C:E.452 pi-Cation interactions: C:F.335 01.50: 25 residues within 4Å: Chain E: F.308, Y.312, Q.317, L.320, L.327, Y.332, F.335, E.336, K.341, Y.342, A.374, G.375, R.376, P.378, E.443, L.445, G.446, S.447, E.452, V.511, F.585, S.586, W.587, F.588 Ligands: MTA.49 17 PLIP interactions: 17 interactions with chain E Hydrophobic interactions: E:Y.312, E:L.320, E:L.327, E:F.335, E:F.335, E:F.335, E:F.335, E:P.378, E:V.511, E:F.585, E:F.588 Hydrogen bonds: E:R.376, E:F.585, E:W.587, E:F.588 Salt bridges: E:E.452 pi-Cation interactions: E:F.335 01.74: 25 residues within 4Å: Chain G: F.308, Y.312, Q.317, L.320, L.327, Y.332, F.335, E.336, K.341, Y.342, A.374, G.375, R.376, P.378, E.443, L.445, G.446, S.447, E.452, V.511, F.585, S.586, W.587, F.588 Ligands: MTA.73 17 PLIP interactions: 17 interactions with chain G Hydrophobic interactions: G:Y.312, G:L.320, G:L.327, G:F.335, G:F.335, G:F.335, G:F.335, G:P.378, G:V.511, G:F.585, G:F.588 Hydrogen bonds: G:R.376, G:F.585, G:W.587, G:F.588 Salt bridges: G:E.452 pi-Cation interactions: G:F.335

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

EDO.3: 7 residues within 4Å: Chain A: E.137, D.138, N.139, T.140, N.199, L.203 Chain C: T.626 Ligand excluded by PLIP EDO.4: 4 residues within 4Å: Chain A: Y.543, C.544, T.545 Chain C: R.108 Ligand excluded by PLIP EDO.5: 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.6: 7 residues within 4Å: Chain A: N.541, R.542, W.611, R.612, C.613 Chain C: E.112, R.144 Ligand excluded by PLIP EDO.7: 4 residues within 4Å: Chain A: L.323, K.401, D.427, L.645 Ligand excluded by PLIP EDO.8: 8 residues within 4Å: Chain A: W.194, D.227, R.228, L.230, S.484, H.518, N.553, T.554 Ligand excluded by PLIP EDO.9: 8 residues within 4Å: Chain G: L.119, G.122, A.123, L.127, F.130, H.149, S.157, F.159 Ligand excluded by PLIP EDO.10: 1 residues within 4Å: Chain A: E.475 Ligand excluded by PLIP EDO.11: 5 residues within 4Å: Chain A: F.54, Q.117, F.121 Chain G: P.403, V.407 Ligand excluded by PLIP EDO.12: 6 residues within 4Å: Chain A: P.233, I.234, K.235, L.268, K.487, N.516 Ligand excluded by PLIP EDO.13: 8 residues within 4Å: Chain A: S.329, Q.330, E.333, R.376 Chain G: D.78, L.81, G.83, W.86 Ligand excluded by PLIP EDO.14: 3 residues within 4Å: Chain A: Q.317, S.318, C.495 Ligand excluded by PLIP EDO.15: 3 residues within 4Å: Chain A: T.545, R.609 Chain C: D.138 Ligand excluded by PLIP EDO.16: 6 residues within 4Å: Chain A: E.105, R.108, R.109, E.112 Chain C: R.542, Y.543 Ligand excluded by PLIP EDO.23: 4 residues within 4Å: Chain A: N.135 Chain B: K.153, A.176, Q.177 Ligand excluded by PLIP EDO.24: 4 residues within 4Å: Chain B: K.126, F.127, C.128, K.129 Ligand excluded by PLIP EDO.27: 7 residues within 4Å: Chain A: T.626 Chain C: E.137, D.138, N.139, T.140, N.199, L.203 Ligand excluded by PLIP EDO.28: 4 residues within 4Å: Chain A: R.108 Chain C: Y.543, C.544, T.545 Ligand excluded by PLIP EDO.29: 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.30: 7 residues within 4Å: Chain A: E.112, R.144 Chain C: N.541, R.542, W.611, R.612, C.613 Ligand excluded by PLIP EDO.31: 4 residues within 4Å: Chain C: L.323, K.401, D.427, L.645 Ligand excluded by PLIP EDO.32: 8 residues within 4Å: Chain C: W.194, D.227, R.228, L.230, S.484, H.518, N.553, T.554 Ligand excluded by PLIP EDO.33: 8 residues within 4Å: Chain E: L.119, G.122, A.123, L.127, F.130, H.149, S.157, F.159 Ligand excluded by PLIP EDO.34: 1 residues within 4Å: Chain C: E.475 Ligand excluded by PLIP EDO.35: 5 residues within 4Å: Chain C: F.54, Q.117, F.121 Chain E: P.403, V.407 Ligand excluded by PLIP EDO.36: 6 residues within 4Å: Chain C: P.233, I.234, K.235, L.268, K.487, N.516 Ligand excluded by PLIP EDO.37: 8 residues within 4Å: Chain C: S.329, Q.330, E.333, R.376 Chain E: D.78, L.81, G.83, W.86 Ligand excluded by PLIP EDO.38: 3 residues within 4Å: Chain C: Q.317, S.318, C.495 Ligand excluded by PLIP EDO.39: 3 residues within 4Å: Chain A: D.138 Chain C: T.545, R.609 Ligand excluded by PLIP EDO.40: 6 residues within 4Å: Chain A: R.542, Y.543 Chain C: E.105, R.108, R.109, E.112 Ligand excluded by PLIP EDO.47: 4 residues within 4Å: Chain C: N.135 Chain D: K.153, A.176, Q.177 Ligand excluded by PLIP EDO.48: 4 residues within 4Å: Chain D: K.126, F.127, C.128, K.129 Ligand excluded by PLIP EDO.51: 7 residues within 4Å: Chain E: E.137, D.138, N.139, T.140, N.199, L.203 Chain G: T.626 Ligand excluded by PLIP EDO.52: 4 residues within 4Å: Chain E: Y.543, C.544, T.545 Chain G: R.108 Ligand excluded by PLIP EDO.53: 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.54: 7 residues within 4Å: Chain E: N.541, R.542, W.611, R.612, C.613 Chain G: E.112, R.144 Ligand excluded by PLIP EDO.55: 4 residues within 4Å: Chain E: L.323, K.401, D.427, L.645 Ligand excluded by PLIP EDO.56: 8 residues within 4Å: Chain E: W.194, D.227, R.228, L.230, S.484, H.518, N.553, T.554 Ligand excluded by PLIP EDO.57: 8 residues within 4Å: Chain C: L.119, G.122, A.123, L.127, F.130, H.149, S.157, F.159 Ligand excluded by PLIP EDO.58: 1 residues within 4Å: Chain E: E.475 Ligand excluded by PLIP EDO.59: 5 residues within 4Å: Chain C: P.403, V.407 Chain E: F.54, Q.117, F.121 Ligand excluded by PLIP EDO.60: 6 residues within 4Å: Chain E: P.233, I.234, K.235, L.268, K.487, N.516 Ligand excluded by PLIP EDO.61: 8 residues within 4Å: Chain C: D.78, L.81, G.83, W.86 Chain E: S.329, Q.330, E.333, R.376 Ligand excluded by PLIP EDO.62: 3 residues within 4Å: Chain E: Q.317, S.318, C.495 Ligand excluded by PLIP EDO.63: 3 residues within 4Å: Chain E: T.545, R.609 Chain G: D.138 Ligand excluded by PLIP EDO.64: 6 residues within 4Å: Chain E: E.105, R.108, R.109, E.112 Chain G: R.542, Y.543 Ligand excluded by PLIP EDO.71: 4 residues within 4Å: Chain E: N.135 Chain F: K.153, A.176, Q.177 Ligand excluded by PLIP EDO.72: 4 residues within 4Å: Chain F: K.126, F.127, C.128, K.129 Ligand excluded by PLIP EDO.75: 7 residues within 4Å: Chain E: T.626 Chain G: E.137, D.138, N.139, T.140, N.199, L.203 Ligand excluded by PLIP EDO.76: 4 residues within 4Å: Chain E: R.108 Chain G: Y.543, C.544, T.545 Ligand excluded by PLIP EDO.77: 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.78: 7 residues within 4Å: Chain E: E.112, R.144 Chain G: N.541, R.542, W.611, R.612, C.613 Ligand excluded by PLIP EDO.79: 4 residues within 4Å: Chain G: L.323, K.401, D.427, L.645 Ligand excluded by PLIP EDO.80: 8 residues within 4Å: Chain G: W.194, D.227, R.228, L.230, S.484, H.518, N.553, T.554 Ligand excluded by PLIP EDO.81: 8 residues within 4Å: Chain A: L.119, G.122, A.123, L.127, F.130, H.149, S.157, F.159 Ligand excluded by PLIP EDO.82: 1 residues within 4Å: Chain G: E.475 Ligand excluded by PLIP EDO.83: 5 residues within 4Å: Chain A: P.403, V.407 Chain G: F.54, Q.117, F.121 Ligand excluded by PLIP EDO.84: 6 residues within 4Å: Chain G: P.233, I.234, K.235, L.268, K.487, N.516 Ligand excluded by PLIP EDO.85: 8 residues within 4Å: Chain A: D.78, L.81, G.83, W.86 Chain G: S.329, Q.330, E.333, R.376 Ligand excluded by PLIP EDO.86: 3 residues within 4Å: Chain G: Q.317, S.318, C.495 Ligand excluded by PLIP EDO.87: 3 residues within 4Å: Chain E: D.138 Chain G: T.545, R.609 Ligand excluded by PLIP EDO.88: 6 residues within 4Å: Chain E: R.542, Y.543 Chain G: E.105, R.108, R.109, E.112 Ligand excluded by PLIP EDO.95: 4 residues within 4Å: Chain G: N.135 Chain H: K.153, A.176, Q.177 Ligand excluded by PLIP EDO.96: 4 residues within 4Å: Chain H: K.126, F.127, C.128, K.129 Ligand excluded by PLIP

16 x NA: SODIUM ION(Non-functional Binders)

NA.17: 2 residues within 4Å: Chain A: Y.489, Q.596 Ligand excluded by PLIP NA.18: 1 residues within 4Å: Chain A: Q.271 Ligand excluded by PLIP NA.19: 1 residues within 4Å: Chain A: T.637 Ligand excluded by PLIP NA.20: 1 residues within 4Å: Chain A: T.642 Ligand excluded by PLIP NA.41: 2 residues within 4Å: Chain C: Y.489, Q.596 Ligand excluded by PLIP NA.42: 1 residues within 4Å: Chain C: Q.271 Ligand excluded by PLIP NA.43: 1 residues within 4Å: Chain C: T.637 Ligand excluded by PLIP NA.44: 1 residues within 4Å: Chain C: T.642 Ligand excluded by PLIP NA.65: 2 residues within 4Å: Chain E: Y.489, Q.596 Ligand excluded by PLIP NA.66: 1 residues within 4Å: Chain E: Q.271 Ligand excluded by PLIP NA.67: 1 residues within 4Å: Chain E: T.637 Ligand excluded by PLIP NA.68: 1 residues within 4Å: Chain E: T.642 Ligand excluded by PLIP NA.89: 2 residues within 4Å: Chain G: Y.489, Q.596 Ligand excluded by PLIP NA.90: 1 residues within 4Å: Chain G: Q.271 Ligand excluded by PLIP NA.91: 1 residues within 4Å: Chain G: T.637 Ligand excluded by PLIP NA.92: 1 residues within 4Å: Chain G: T.642 Ligand excluded by PLIP

4 x GOL: GLYCEROL(Non-functional Binders)

GOL.21: 4 residues within 4Å: Chain A: I.150, H.154, S.207, R.209 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:S.207, A:R.209, A:R.209 GOL.45: 4 residues within 4Å: Chain C: I.150, H.154, S.207, R.209 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:S.207, C:R.209, C:R.209 GOL.69: 4 residues within 4Å: Chain E: I.150, H.154, S.207, R.209 3 PLIP interactions: 3 interactions with chain E Hydrogen bonds: E:S.207, E:R.209, E:R.209 GOL.93: 4 residues within 4Å: Chain G: I.150, H.154, S.207, R.209 3 PLIP interactions: 3 interactions with chain G Hydrogen bonds: G:S.207, G:R.209, G:R.209

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

CL.22: 1 residues within 4Å: Chain A: H.580 Ligand excluded by PLIP CL.46: 1 residues within 4Å: Chain C: H.580 Ligand excluded by PLIP CL.70: 1 residues within 4Å: Chain E: H.580 Ligand excluded by PLIP CL.94: 1 residues within 4Å: Chain G: H.580 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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