SMTL ID : 8g2h.1

Crystal Structure of PRMT4 with Compound YD1113

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.49 Å

Oligo State

homo-dimer

Ligands

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

YVU.1: 25 residues within 4Å: Chain A: Y.28, F.29, Y.32, Q.38, M.41, M.42, R.47, T.48, Y.51, G.71, C.72, G.73, I.76, L.77, E.93, A.94, S.95, G.119, K.120, V.121, E.122, E.136, M.147, S.150 Ligands: UNX.9 21 PLIP interactions: 21 interactions with chain A Hydrophobic interactions: A:R.47, A:Y.51, A:Y.51, A:I.76, A:L.77, A:L.77, A:E.136 Hydrogen bonds: A:Y.28, A:Q.38, A:R.47, A:R.47, A:G.71, A:C.72, A:A.94, A:V.121, A:E.122, A:S.150 Water bridges: A:S.74, A:L.77 pi-Stacking: A:F.29 pi-Cation interactions: A:R.47 YVU.10: 25 residues within 4Å: Chain B: Y.28, F.29, Y.32, Q.38, M.41, M.42, R.47, T.48, Y.51, G.71, C.72, G.73, I.76, L.77, E.93, A.94, S.95, G.119, K.120, V.121, E.122, E.136, M.147, S.150 Ligands: UNX.18 20 PLIP interactions: 20 interactions with chain B Hydrophobic interactions: B:R.47, B:Y.51, B:Y.51, B:I.76, B:L.77, B:L.77, B:E.136 Hydrogen bonds: B:Q.38, B:R.47, B:R.47, B:G.71, B:C.72, B:A.94, B:V.121, B:E.122, B:S.150 Water bridges: B:S.74, B:L.77 pi-Stacking: B:F.29 pi-Cation interactions: B:R.47

4 x GOL: GLYCEROL(Non-functional Binders)

GOL.2: 5 residues within 4Å: Chain A: F.186, D.211, F.214, Q.302 Ligands: NA.4 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:D.211, A:D.211, A:Q.302 Water bridges: A:D.211, A:Q.302 GOL.3: 2 residues within 4Å: Chain A: R.225, I.226 No protein-ligand interaction detected (PLIP) GOL.11: 5 residues within 4Å: Chain B: F.186, D.211, F.214, Q.302 Ligands: NA.13 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:D.211, B:Q.302 Water bridges: B:D.211, B:Q.302 GOL.12: 2 residues within 4Å: Chain B: R.225, I.226 No protein-ligand interaction detected (PLIP)

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

NA.4: 2 residues within 4Å: Chain A: Q.302 Ligands: GOL.2 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Q.302 NA.13: 2 residues within 4Å: Chain B: Q.302 Ligands: GOL.11 No protein-ligand interaction detected (PLIP)

10 x UNX: UNKNOWN ATOM OR ION(Non-functional Binders)

UNX.5: 2 residues within 4Å: Chain A: R.146, S.150 No protein-ligand interaction detected (PLIP) UNX.6: 2 residues within 4Å: Chain A: D.245, R.248 No protein-ligand interaction detected (PLIP) UNX.7: 2 residues within 4Å: Chain A: E.136, M.138 No protein-ligand interaction detected (PLIP) UNX.8: 1 residues within 4Å: Chain A: E.179 No protein-ligand interaction detected (PLIP) UNX.9: 8 residues within 4Å: Chain A: D.69, V.70, G.71, C.72, L.77, S.135, E.136 Ligands: YVU.1 No protein-ligand interaction detected (PLIP) UNX.14: 2 residues within 4Å: Chain B: R.146, S.150 No protein-ligand interaction detected (PLIP) UNX.15: 2 residues within 4Å: Chain B: D.245, R.248 No protein-ligand interaction detected (PLIP) UNX.16: 2 residues within 4Å: Chain B: E.136, M.138 No protein-ligand interaction detected (PLIP) UNX.17: 1 residues within 4Å: Chain B: E.179 No protein-ligand interaction detected (PLIP) UNX.18: 8 residues within 4Å: Chain B: D.69, V.70, G.71, C.72, L.77, S.135, E.136 Ligands: YVU.10 No protein-ligand interaction detected (PLIP)

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

2023-12-13

Peptides

Histone-arginine methyltransferase CARM1: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

Histone-arginine methyltransferase CARM1

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