SMTL ID : 5wfc.1

Humanized mutant of the Chaetomium thermophilum Polycomb Repressive Complex 2 bound to the inhibitor GSK343

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.28 Å

Oligo State

hetero-1-1-1-mer

Ligands

8 x ZN: ZINC ION(Non-covalent)

ZN.1: 6 residues within 4Å: Chain B: C.546, C.567, C.574, C.579 Ligands: ZN.2, ZN.3 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:C.546, B:C.567, B:C.574, B:C.579 ZN.2: 7 residues within 4Å: Chain B: C.546, C.555, C.574, C.582, C.603 Ligands: ZN.1, ZN.3 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:C.555, B:C.574, B:C.582, B:C.603 ZN.3: 7 residues within 4Å: Chain B: C.546, C.548, C.555, C.565, C.574 Ligands: ZN.1, ZN.2 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:C.546, B:C.548, B:C.555, B:C.565 ZN.4: 7 residues within 4Å: Chain B: C.504, H.506, C.510, C.516, C.528 Ligands: ZN.5, ZN.6 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:C.504, B:H.506, B:C.510, B:C.516 ZN.5: 6 residues within 4Å: Chain B: C.510, C.528, C.534, C.539 Ligands: ZN.4, ZN.6 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:C.510, B:C.528, B:C.534, B:C.539 ZN.6: 6 residues within 4Å: Chain B: C.504, C.518, C.528, C.532 Ligands: ZN.4, ZN.5 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:C.504, B:C.518, B:C.528, B:C.532 ZN.7: 4 residues within 4Å: Chain B: C.327, C.330, C.335, H.337 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:C.327, B:C.330, B:C.335, B:H.337 ZN.8: 5 residues within 4Å: Chain B: C.389, C.393, Y.394, C.434, C.444 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:C.389, B:C.393, B:C.434, B:C.444

1 x A97: N-[(6-methyl-2-oxo-4-propyl-1,2-dihydropyridin-3-yl)methyl]-6-[2-(4-methylpiperazin-1-yl)pyridin-4-yl]-1-(propan-2-yl)-1H-indazole-4-carboxamide(Non-covalent)

A97.9: 13 residues within 4Å: Chain B: I.121, Y.122, Y.123, H.126, G.627, Y.628, R.662, A.687, A.688, R.695, Y.696, I.697, N.698 11 PLIP interactions: 11 interactions with chain B Hydrophobic interactions: B:I.121, B:Y.123, B:Y.123, B:Y.696, B:Y.696 Hydrogen bonds: B:Y.123, B:G.627, B:Y.628, B:Y.628 Water bridges: B:I.121, B:N.698

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Bratkowski, M. et al., An Evolutionarily Conserved Structural Platform for PRC2 Inhibition by a Class of Ezh2 Inhibitors. Sci Rep (2018)

Release Date

2018-06-27

Peptides

Polycomb Protein EED: A
Histone-lysine-N-methyltransferase EZH2, Polycomb protein SUZ12 chimera: B
Histone H3.1: C

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
D

Polycomb Protein EED

Histone-lysine-N-methyltransferase EZH2, Polycomb protein SUZ12 chimera

Histone H3.1

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