SMTL ID : 6v0p.1

PRMT5 complex bound to covalent PBM inhibitor BRD6711

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.88 Å

Oligo State

hetero-4-4-mer

Ligands

4 x QN4: 2-(5-chloro-6-oxopyridazin-1(6H)-yl)-N-(4-methyl-3-sulfamoylphenyl)acetamide(Covalent)

QN4.1: 10 residues within 4Å: Chain A: N.239, F.243, P.244, V.245, E.276, C.278, S.279, Q.282, Y.283, Y.286 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:F.243, A:V.245, A:Y.283 Hydrogen bonds: A:N.239, A:Q.282, A:Y.286 pi-Stacking: A:F.243 QN4.7: 10 residues within 4Å: Chain C: N.239, F.243, P.244, V.245, E.276, C.278, S.279, Q.282, Y.283, Y.286 7 PLIP interactions: 7 interactions with chain C Hydrophobic interactions: C:F.243, C:V.245, C:Y.283 Hydrogen bonds: C:N.239, C:Q.282, C:Y.286 pi-Stacking: C:F.243 QN4.13: 10 residues within 4Å: Chain E: N.239, F.243, P.244, V.245, E.276, C.278, S.279, Q.282, Y.283, Y.286 7 PLIP interactions: 7 interactions with chain E Hydrophobic interactions: E:F.243, E:V.245, E:Y.283 Hydrogen bonds: E:N.239, E:Q.282, E:Y.286 pi-Stacking: E:F.243 QN4.19: 10 residues within 4Å: Chain G: N.239, F.243, P.244, V.245, E.276, C.278, S.279, Q.282, Y.283, Y.286 7 PLIP interactions: 7 interactions with chain G Hydrophobic interactions: G:F.243, G:V.245, G:Y.283 Hydrogen bonds: G:N.239, G:Q.282, G:Y.286 pi-Stacking: G:F.243

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

CL.2: 4 residues within 4Å: Chain A: R.368, G.369, P.370, N.373 Ligand excluded by PLIP CL.3: 3 residues within 4Å: Chain A: S.199, K.200, R.485 Ligand excluded by PLIP CL.8: 4 residues within 4Å: Chain C: R.368, G.369, P.370, N.373 Ligand excluded by PLIP CL.9: 3 residues within 4Å: Chain C: S.199, K.200, R.485 Ligand excluded by PLIP CL.14: 4 residues within 4Å: Chain E: R.368, G.369, P.370, N.373 Ligand excluded by PLIP CL.15: 3 residues within 4Å: Chain E: S.199, K.200, R.485 Ligand excluded by PLIP CL.20: 4 residues within 4Å: Chain G: R.368, G.369, P.370, N.373 Ligand excluded by PLIP CL.21: 3 residues within 4Å: Chain G: S.199, K.200, R.485 Ligand excluded by PLIP

4 x SFG: SINEFUNGIN(Non-covalent)

SFG.4: 25 residues within 4Å: Chain A: P.314, L.315, L.319, Y.324, F.327, E.328, K.333, Y.334, G.365, A.366, G.367, P.370, L.371, V.391, E.392, K.393, N.394, S.418, D.419, M.420, R.421, E.435, L.436, E.444, C.449 17 PLIP interactions: 17 interactions with chain A Hydrophobic interactions: A:Y.324, A:F.327 Hydrogen bonds: A:Y.324, A:Y.324, A:G.365, A:G.367, A:K.393, A:D.419, A:M.420, A:R.421, A:E.435 Water bridges: A:L.371, A:N.394, A:E.435, A:E.444 Salt bridges: A:K.333 pi-Cation interactions: A:K.393 SFG.10: 25 residues within 4Å: Chain C: P.314, L.315, L.319, Y.324, F.327, E.328, K.333, Y.334, G.365, A.366, G.367, P.370, L.371, V.391, E.392, K.393, N.394, S.418, D.419, M.420, R.421, E.435, L.436, E.444, C.449 17 PLIP interactions: 17 interactions with chain C Hydrophobic interactions: C:Y.324, C:F.327 Hydrogen bonds: C:Y.324, C:Y.324, C:G.365, C:G.367, C:K.393, C:D.419, C:M.420, C:R.421, C:E.435 Water bridges: C:L.371, C:N.394, C:E.435, C:E.444 Salt bridges: C:K.333 pi-Cation interactions: C:K.393 SFG.16: 25 residues within 4Å: Chain E: P.314, L.315, L.319, Y.324, F.327, E.328, K.333, Y.334, G.365, A.366, G.367, P.370, L.371, V.391, E.392, K.393, N.394, S.418, D.419, M.420, R.421, E.435, L.436, E.444, C.449 16 PLIP interactions: 16 interactions with chain E Hydrophobic interactions: E:Y.324, E:F.327 Hydrogen bonds: E:Y.324, E:Y.324, E:G.365, E:G.367, E:K.393, E:D.419, E:M.420, E:R.421, E:E.435 Water bridges: E:L.371, E:N.394, E:E.435 Salt bridges: E:K.333 pi-Cation interactions: E:K.393 SFG.22: 25 residues within 4Å: Chain G: P.314, L.315, L.319, Y.324, F.327, E.328, K.333, Y.334, G.365, A.366, G.367, P.370, L.371, V.391, E.392, K.393, N.394, S.418, D.419, M.420, R.421, E.435, L.436, E.444, C.449 16 PLIP interactions: 16 interactions with chain G Hydrophobic interactions: G:Y.324, G:F.327 Hydrogen bonds: G:Y.324, G:Y.324, G:G.365, G:G.367, G:K.393, G:D.419, G:M.420, G:R.421, G:E.435 Water bridges: G:L.371, G:N.394, G:E.435 Salt bridges: G:K.333 pi-Cation interactions: G:K.393

8 x GOL: GLYCEROL(Non-functional Binders)

GOL.5: 8 residues within 4Å: Chain A: D.39, F.40, T.80, V.83, P.120, A.121, W.152, Q.263 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Q.263, A:Q.263 GOL.6: 6 residues within 4Å: Chain A: Q.454, L.457, K.458, D.459, P.524, R.526 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Q.454, A:R.526, A:R.526 GOL.11: 8 residues within 4Å: Chain C: D.39, F.40, T.80, V.83, P.120, A.121, W.152, Q.263 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:Q.263, C:Q.263 GOL.12: 6 residues within 4Å: Chain C: Q.454, L.457, K.458, D.459, P.524, R.526 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:Q.454, C:R.526, C:R.526 GOL.17: 8 residues within 4Å: Chain E: D.39, F.40, T.80, V.83, P.120, A.121, W.152, Q.263 2 PLIP interactions: 2 interactions with chain E Hydrogen bonds: E:Q.263, E:Q.263 GOL.18: 6 residues within 4Å: Chain E: Q.454, L.457, K.458, D.459, P.524, R.526 3 PLIP interactions: 3 interactions with chain E Hydrogen bonds: E:Q.454, E:R.526, E:R.526 GOL.23: 8 residues within 4Å: Chain G: D.39, F.40, T.80, V.83, P.120, A.121, W.152, Q.263 2 PLIP interactions: 2 interactions with chain G Hydrogen bonds: G:Q.263, G:Q.263 GOL.24: 6 residues within 4Å: Chain G: Q.454, L.457, K.458, D.459, P.524, R.526 3 PLIP interactions: 3 interactions with chain G Hydrogen bonds: G:Q.454, G:R.526, G:R.526

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

McKinney, D.C. et al., Discovery of a First-in-Class Inhibitor of the PRMT5-Substrate Adaptor Interaction. J.Med.Chem. (2021)

Release Date

2020-11-25

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

Related Entries With Identical Sequence