SMTL ID : 9eyv.1

Human PRMT5 in complex with AZ compound 12

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.15 Å

Oligo State

hetero-4-4-mer

Ligands

4 x 01: (1~{S})-~{N}-[(4-fluorophenyl)methyl]-3-oxidanylidene-2-(1~{H}-pyrrolo[3,2-b]pyridin-2-ylmethyl)-1~{H}-isoindole-1-carboxamide

01.1: 18 residues within 4Å: Chain A: Y.304, Q.309, S.310, P.311, L.312, F.327, K.333, E.435, L.437, G.438, S.439, E.444, V.503, F.577, S.578, W.579, F.580 Ligands: MTA.2 13 PLIP interactions: 13 interactions with chain A Hydrophobic interactions: A:Y.304, A:L.312, A:L.312, A:F.327, A:V.503, A:F.580, A:F.580 Hydrogen bonds: A:L.312, A:K.333, A:S.439, A:F.580 Water bridges: A:E.444 pi-Stacking: A:F.327 01.4: 18 residues within 4Å: Chain C: Y.304, Q.309, S.310, P.311, L.312, F.327, K.333, E.435, L.437, G.438, S.439, E.444, V.503, F.577, S.578, W.579, F.580 Ligands: MTA.5 13 PLIP interactions: 13 interactions with chain C Hydrophobic interactions: C:Y.304, C:L.312, C:L.312, C:F.327, C:V.503, C:F.580, C:F.580 Hydrogen bonds: C:L.312, C:K.333, C:S.439, C:F.580 Water bridges: C:E.444 pi-Stacking: C:F.327 01.7: 18 residues within 4Å: Chain E: Y.304, Q.309, S.310, P.311, L.312, F.327, K.333, E.435, L.437, G.438, S.439, E.444, V.503, F.577, S.578, W.579, F.580 Ligands: MTA.8 12 PLIP interactions: 12 interactions with chain E Hydrophobic interactions: E:Y.304, E:L.312, E:L.312, E:F.327, E:V.503, E:F.580, E:F.580 Hydrogen bonds: E:L.312, E:K.333, E:S.439, E:F.580 pi-Stacking: E:F.327 01.10: 18 residues within 4Å: Chain G: Y.304, Q.309, S.310, P.311, L.312, F.327, K.333, E.435, L.437, G.438, S.439, E.444, V.503, F.577, S.578, W.579, F.580 Ligands: MTA.11 12 PLIP interactions: 12 interactions with chain G Hydrophobic interactions: G:Y.304, G:L.312, G:L.312, G:F.327, G:V.503, G:F.580, G:F.580 Hydrogen bonds: G:L.312, G:K.333, G:S.439, G:F.580 pi-Stacking: G:F.327

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

MTA.2: 16 residues within 4Å: Chain A: P.314, L.315, Y.324, G.365, G.367, E.392, K.393, N.394, S.418, D.419, M.420, R.421, E.435, L.436, C.449 Ligands: 01.1 8 PLIP interactions: 8 interactions with chain A Hydrogen bonds: A:Y.324, A:G.367, A:K.393, A:D.419, A:M.420 Water bridges: A:N.394, A:N.394 pi-Cation interactions: A:K.393 MTA.5: 16 residues within 4Å: Chain C: P.314, L.315, Y.324, G.365, G.367, E.392, K.393, N.394, S.418, D.419, M.420, R.421, E.435, L.436, C.449 Ligands: 01.4 8 PLIP interactions: 8 interactions with chain C Hydrogen bonds: C:Y.324, C:G.367, C:K.393, C:D.419, C:M.420 Water bridges: C:N.394, C:N.394 pi-Cation interactions: C:K.393 MTA.8: 16 residues within 4Å: Chain E: P.314, L.315, Y.324, G.365, G.367, E.392, K.393, N.394, S.418, D.419, M.420, R.421, E.435, L.436, C.449 Ligands: 01.7 9 PLIP interactions: 9 interactions with chain E Hydrogen bonds: E:Y.324, E:Y.324, E:G.367, E:K.393, E:D.419, E:M.420 Water bridges: E:N.394, E:N.394 pi-Cation interactions: E:K.393 MTA.11: 16 residues within 4Å: Chain G: P.314, L.315, Y.324, G.365, G.367, E.392, K.393, N.394, S.418, D.419, M.420, R.421, E.435, L.436, C.449 Ligands: 01.10 9 PLIP interactions: 9 interactions with chain G Hydrogen bonds: G:Y.324, G:Y.324, G:G.367, G:K.393, G:D.419, G:M.420 Water bridges: G:N.394, G:N.394 pi-Cation interactions: G:K.393

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

SO4.3: 6 residues within 4Å: Chain A: F.40, T.80, V.83, P.120, W.152, Q.263 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:T.80, A:Q.263, A:Q.263 SO4.6: 6 residues within 4Å: Chain C: F.40, T.80, V.83, P.120, W.152, Q.263 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:T.80, C:Q.263, C:Q.263 SO4.9: 6 residues within 4Å: Chain E: F.40, T.80, V.83, P.120, W.152, Q.263 3 PLIP interactions: 3 interactions with chain E Hydrogen bonds: E:T.80, E:Q.263, E:Q.263 SO4.12: 6 residues within 4Å: Chain G: F.40, T.80, V.83, P.120, W.152, Q.263 3 PLIP interactions: 3 interactions with chain G Hydrogen bonds: G:T.80, G:Q.263, G:Q.263

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Smith, J.M. et al., Discovery and In Vivo Efficacy of AZ-PRMT5i-1, a Novel PRMT5 Inhibitor with High MTA Cooperativity. J.Med.Chem. (2024)

Release Date

2024-08-14

Peptides

Protein arginine N-methyltransferase 5, N-terminally processed: ACEG
Methylosome protein WDR77: 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, N-terminally processed

Methylosome protein WDR77

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