SMTL ID : 8g2g.1 (1 other biounit)

Crystal structure of PRMT3 with compound YD1113

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.02 Å

Oligo State

homo-dimer

Ligands

2 x YVU: 5'-S-[2-(benzylcarbamamido)ethyl]-5'-thioadenosine(Non-covalent)

YVU.1: 23 residues within 4Å: Chain A: Y.29, F.30, Y.33, H.39, M.42, R.48, T.49, Y.52, G.72, C.73, G.74, I.77, L.78, D.94, Q.95, S.96, G.120, K.121, I.122, E.123, E.138, M.149, S.152 22 PLIP interactions: 22 interactions with chain A Hydrophobic interactions: A:T.49, A:Y.52, A:I.77, A:L.78, A:L.78, A:E.138 Hydrogen bonds: A:R.48, A:R.48, A:G.72, A:C.73, A:Q.95, A:S.96, A:I.122, A:E.123, A:S.152 Water bridges: A:T.75, A:T.75, A:L.78 pi-Stacking: A:F.30, A:F.30, A:Y.52 pi-Cation interactions: A:R.48 YVU.4: 23 residues within 4Å: Chain B: Y.29, F.30, Y.33, H.39, M.42, R.48, T.49, Y.52, G.72, C.73, G.74, I.77, L.78, D.94, Q.95, S.96, G.120, K.121, I.122, E.123, E.138, M.149, S.152 22 PLIP interactions: 22 interactions with chain B Hydrophobic interactions: B:T.49, B:Y.52, B:I.77, B:L.78, B:L.78, B:E.138 Hydrogen bonds: B:R.48, B:R.48, B:G.72, B:C.73, B:Q.95, B:S.96, B:I.122, B:E.123, B:S.152 Water bridges: B:H.39, B:T.75, B:L.78 pi-Stacking: B:F.30, B:F.30, B:Y.52 pi-Cation interactions: B:R.48

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

SO4.2: 3 residues within 4Å: Chain A: V.129, E.130, K.131 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:E.130, A:K.131 SO4.3: 3 residues within 4Å: Chain A: E.214, V.215, K.290 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:V.215 Salt bridges: A:K.290 SO4.5: 3 residues within 4Å: Chain B: V.129, E.130, K.131 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:E.130, B:K.131 SO4.6: 3 residues within 4Å: Chain B: E.214, V.215, K.290 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:V.215 Salt bridges: B:K.290

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Deng, Y. et al., A unique binding pocket induced by a noncanonical SAH mimic to develop potent and selective PRMT inhibitors. Acta Pharm Sin B (2023)

Release Date

2023-04-26

Peptides

Protein arginine N-methyltransferase 3: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

Protein arginine N-methyltransferase 3

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