SMTL ID : 9mgm.1

Crystal structure of PRMT5:MEP50 in complex with MTA and compound 24

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.25 Å

Oligo State

hetero-4-4-mer

Ligands

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

MTA.1: 14 residues within 4Å: Chain A: L.323, Y.332, G.373, G.375, E.400, K.401, N.402, S.426, D.427, M.428, 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:K.401, A:D.427, A:M.428 Water bridges: A:N.402 pi-Cation interactions: A:K.401 MTA.4: 14 residues within 4Å: Chain C: L.323, Y.332, G.373, G.375, E.400, K.401, N.402, S.426, D.427, M.428, E.443, L.444, C.457 Ligands: 01.5 7 PLIP interactions: 7 interactions with chain C Hydrogen bonds: C:Y.332, C:Y.332, C:K.401, C:D.427, C:M.428 Water bridges: C:N.402 pi-Cation interactions: C:K.401 MTA.7: 14 residues within 4Å: Chain E: L.323, Y.332, G.373, G.375, E.400, K.401, N.402, S.426, D.427, M.428, E.443, L.444, C.457 Ligands: 01.8 6 PLIP interactions: 6 interactions with chain E Hydrogen bonds: E:Y.332, E:K.401, E:D.427, E:M.428 Water bridges: E:N.402 pi-Cation interactions: E:K.401 MTA.10: 14 residues within 4Å: Chain G: L.323, Y.332, G.373, G.375, E.400, K.401, N.402, S.426, D.427, M.428, E.443, L.444, C.457 Ligands: 01.11 6 PLIP interactions: 6 interactions with chain G Hydrogen bonds: G:Y.332, G:K.401, G:D.427, G:M.428 Water bridges: G:N.402 pi-Cation interactions: G:K.401

4 x 01: 2-(cyclobutylamino)-N-[(2S)-2-hydroxy-3-{6-[(1-methyl-1H-pyrazol-5-yl)methoxy]-3,4-dihydroisoquinolin-2(1H)-yl}propyl]pyridine-4-carboxamide

01.2: 24 residues within 4Å: Chain A: F.308, Y.312, Q.317, L.327, T.331, Y.332, F.335, E.336, K.341, Y.342, 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.1 19 PLIP interactions: 19 interactions with chain A Hydrophobic interactions: A:Y.312, A:L.327, A:T.331, A:Y.332, A:F.335, A:E.336, A:F.585, A:F.588, A:F.588 Hydrogen bonds: A:R.376, A:S.447, A:E.452, A:F.585, A:F.588 Water bridges: A:Q.317 Salt bridges: A:E.452 pi-Stacking: A:F.335, A:F.335 pi-Cation interactions: A:F.335 01.5: 24 residues within 4Å: Chain C: F.308, Y.312, Q.317, L.327, T.331, Y.332, F.335, E.336, K.341, Y.342, 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.4 19 PLIP interactions: 19 interactions with chain C Hydrophobic interactions: C:Y.312, C:L.327, C:T.331, C:Y.332, C:F.335, C:E.336, C:F.585, C:F.588, C:F.588 Hydrogen bonds: C:R.376, C:S.447, C:E.452, C:F.585, C:F.588 Water bridges: C:Q.317 Salt bridges: C:E.452 pi-Stacking: C:F.335, C:F.335 pi-Cation interactions: C:F.335 01.8: 24 residues within 4Å: Chain E: F.308, Y.312, Q.317, L.327, T.331, Y.332, F.335, E.336, K.341, Y.342, 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.7 20 PLIP interactions: 20 interactions with chain E Hydrophobic interactions: E:Y.312, E:L.327, E:T.331, E:Y.332, E:F.335, E:E.336, E:F.585, E:F.588, E:F.588 Hydrogen bonds: E:R.376, E:S.447, E:E.452, E:F.585, E:F.588 Water bridges: E:Q.317, E:E.452 Salt bridges: E:E.452 pi-Stacking: E:F.335, E:F.335 pi-Cation interactions: E:F.335 01.11: 24 residues within 4Å: Chain G: F.308, Y.312, Q.317, L.327, T.331, Y.332, F.335, E.336, K.341, Y.342, 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.10 20 PLIP interactions: 20 interactions with chain G Hydrophobic interactions: G:Y.312, G:L.327, G:T.331, G:Y.332, G:F.335, G:E.336, G:F.585, G:F.588, G:F.588 Hydrogen bonds: G:R.376, G:S.447, G:E.452, G:F.585, G:F.588 Water bridges: G:Q.317, G:E.452 Salt bridges: G:E.452 pi-Stacking: G:F.335, G:F.335 pi-Cation interactions: G:F.335

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

SO4.3: 5 residues within 4Å: Chain A: Y.206, S.207, K.208, N.490, R.493 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:S.207, A:K.208 Water bridges: A:R.493, A:R.493 Salt bridges: A:R.493 SO4.6: 5 residues within 4Å: Chain C: Y.206, S.207, K.208, N.490, R.493 5 PLIP interactions: 5 interactions with chain C Hydrogen bonds: C:S.207, C:K.208 Water bridges: C:R.493, C:R.493 Salt bridges: C:R.493 SO4.9: 5 residues within 4Å: Chain E: Y.206, S.207, K.208, N.490, R.493 5 PLIP interactions: 5 interactions with chain E Hydrogen bonds: E:S.207, E:K.208 Water bridges: E:R.493, E:R.493 Salt bridges: E:R.493 SO4.12: 5 residues within 4Å: Chain G: Y.206, S.207, K.208, N.490, R.493 5 PLIP interactions: 5 interactions with chain G Hydrogen bonds: G:S.207, G:K.208 Water bridges: G:R.493, G:R.493 Salt bridges: G:R.493

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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