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

Crystal structure of HDAC8 in complex with compound 3

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.70 Å

Oligo State

monomer

Ligands

1 x M8G: N-{2-[(1E)-3-(hydroxyamino)-3-oxoprop-1-en-1-yl]phenyl}-2-phenoxybenzamide(Non-covalent)

M8G.1: 15 residues within 4Å: Chain A: K.57, Y.124, D.125, H.166, H.167, G.175, F.176, D.202, H.204, F.232, D.291, M.298, G.328, Y.330 Ligands: ZN.2 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:K.57, A:Y.124, A:F.176, A:Y.330 Hydrogen bonds: A:H.167, A:Y.330 pi-Stacking: A:F.232, A:Y.330

1 x ZN: ZINC ION(Non-covalent)

ZN.2: 4 residues within 4Å: Chain A: D.202, H.204, D.291 Ligands: M8G.1 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.3: 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.2 K.4: 7 residues within 4Å: Chain A: D.200, L.201, 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

3 x GOL: GLYCEROL(Non-functional Binders)

GOL.5: 4 residues within 4Å: Chain A: A.92, F.94, H.95, T.96 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:H.95 GOL.6: 6 residues within 4Å: Chain A: S.239, D.240, V.241, G.242, L.243 Ligands: GOL.7 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:V.241, A:G.242 GOL.7: 6 residues within 4Å: Chain A: T.235, G.236, D.237, S.239, D.240 Ligands: GOL.6 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:G.236, A:D.237, A:S.239, A:D.240, A:D.240

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

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