SMTL ID : 5ls6.4 (3 other biounits)

Structure of Human Polycomb Repressive Complex 2 (PRC2) with inhibitor

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 3.47 Å

Oligo State

hetero-1-1-1-1-mer

Ligands

8 x ZN: ZINC ION(Non-covalent)

ZN.1: 4 residues within 4Å: Chain A: C.268, C.271, C.276, H.279 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.268, A:C.271, A:C.276, A:H.279 ZN.2: 4 residues within 4Å: Chain A: C.302, C.306, C.401, C.412 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:C.302, A:C.306, A:C.412 ZN.3: 5 residues within 4Å: Chain A: C.479, C.492, C.498, C.502 Ligands: ZN.4 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.479, A:C.492, A:C.498, A:C.502 ZN.4: 6 residues within 4Å: Chain A: C.472, H.474, C.479, C.483 Ligands: ZN.3, ZN.5 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.472, A:H.474, A:C.479, A:C.483 ZN.5: 5 residues within 4Å: Chain A: C.472, C.485, C.492, C.496 Ligands: ZN.4 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:C.472, A:C.485, A:C.496 ZN.6: 6 residues within 4Å: Chain A: C.509, C.515, C.529, C.537, C.550 Ligands: ZN.8 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.515, A:C.529, A:C.537, A:C.550 ZN.7: 5 residues within 4Å: Chain A: C.509, C.522, C.529, C.534 Ligands: ZN.8 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.509, A:C.522, A:C.529, A:C.534 ZN.8: 7 residues within 4Å: Chain A: C.509, C.511, C.515, C.520, C.529 Ligands: ZN.6, ZN.7 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.509, A:C.511, A:C.515, A:C.520

1 x 74D: 1-[(1~{R})-1-[1-[2,2-bis(fluoranyl)propyl]piperidin-4-yl]ethyl]-~{N}-[(4-methoxy-6-methyl-2-oxidanylidene-3~{H}-pyridin-3-yl)methyl]-2-methyl-indole-3-carboxamide(Non-covalent)

74D.9: 17 residues within 4Å: Chain A: I.119, M.120, Y.121, P.142, G.572, W.573, Y.607, Y.610, C.612, F.614, R.634, F.635, A.636, N.637 Chain B: H.139, R.162, D.163 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:P.142, A:Y.607, A:Y.610, A:F.614 Hydrogen bonds: A:Y.121, A:W.573, A:N.637 pi-Stacking: A:Y.121

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Vaswani, R.G. et al., Identification of (R)-N-((4-Methoxy-6-methyl-2-oxo-1,2-dihydropyridin-3-yl)methyl)-2-methyl-1-(1-(1-(2,2,2-trifluoroethyl)piperidin-4-yl)ethyl)-1H-indole-3-carboxamide (CPI-1205), a Potent and Selective Inhibitor of Histone Methyltransferase EZH2, Suitable for Phase I Clinical Trials for B-Cell Lymphomas. J. Med. Chem. (2016)

Release Date

2017-02-22

Peptides

Histone-lysine N-methyltransferase EZH2,Histone-lysine N-methyltransferase EZH2,Histone-lysine N-methyltransferase EZH2: A
Polycomb protein EED: B
Polycomb protein SUZ12: C
Jarid2 K116me3: D

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
J

B
K

C
L

D
T

Histone-lysine N-methyltransferase EZH2,Histone-lysine N-methyltransferase EZH2,Histone-lysine N-methyltransferase EZH2

Polycomb protein EED

Polycomb protein SUZ12

Jarid2 K116me3

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