SMTL ID : 6odc.1 (2 other biounits)

Crystal structure of HDAC8 in complex with compound 30

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.80 Å

Oligo State

monomer

Ligands

1 x ZN: ZINC ION(Non-covalent)

ZN.1: 4 residues within 4Å: Chain A: D.202, H.204, D.291 Ligands: M7Y.4 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:D.202, A:H.204, A:D.291

2 x K: POTASSIUM ION(Non-covalent)

K.2: 4 residues within 4Å: Chain A: F.213, T.216, V.219, Y.249 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:T.216, A:V.219, A:Y.249, H2O.1, H2O.1 K.3: 6 residues within 4Å: Chain A: D.200, D.202, H.204, S.223, L.224, H.225 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:D.200, A:D.200, A:D.202, A:H.204, A:S.223

1 x M7Y: (2E)-3-[2-(3-cyclopentyl-5,5-dimethyl-2-oxoimidazolidin-1-yl)phenyl]-N-hydroxyprop-2-enamide(Non-covalent)

M7Y.4: 14 residues within 4Å: Chain A: D.125, H.166, H.167, G.175, F.176, D.202, H.204, F.232, D.291, P.297, M.298, G.328, Y.330 Ligands: ZN.1 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:F.176, A:P.297, A:Y.330 Hydrogen bonds: A:H.167, A:G.328 pi-Stacking: A:F.232, A:Y.330

3 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.5: 4 residues within 4Å: Chain A: Y.248, Y.392, N.396, H.399 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Y.248, A:N.396 EDO.6: 2 residues within 4Å: Chain A: G.123, Y.124 No protein-ligand interaction detected (PLIP) EDO.7: 3 residues within 4Å: Chain A: G.295, N.334, T.373 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.334

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Zheng, X. et al., Structure-based Discovery of Novel N-(E)-N-Hydroxy-3-(2-(2-oxoimidazolidin-1-yl)phenyl)acrylamides as Potent and Selective HDAC8 inhibitors. To Be Published

Release Date

2020-04-01

Peptides

Histone deacetylase 8: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Histone deacetylase 8

Related Entries With Identical Sequence