SMTL ID : 6hqy.4 (3 other biounits)

Crystal structure of Schistosoma mansoni HDAC8 complexed with PCI-34051

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.50 Å

Oligo State

monomer

Ligands

1 x ZN: ZINC ION(Non-covalent)

ZN.1: 4 residues within 4Å: Chain A: D.187, H.189, D.286 Ligands: GKW.4 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:D.187, A:H.189, A:D.286

2 x K: POTASSIUM ION(Non-covalent)

K.2: 7 residues within 4Å: Chain A: D.185, L.186, D.187, H.189, S.208, V.209, H.210 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:D.185, A:D.185, A:D.187, A:H.189, A:V.209 K.3: 4 residues within 4Å: Chain A: F.198, S.201, V.204, S.244 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:F.198, A:S.201, A:V.204, A:S.244, H2O.1

1 x GKW: 1-[(4-methoxyphenyl)methyl]-~{N}-oxidanyl-indole-6-carboxamide(Non-covalent)

GKW.4: 13 residues within 4Å: Chain A: K.21, D.101, H.142, H.143, D.187, H.189, F.217, D.286, P.292, H.293, G.340, Y.342 Ligands: ZN.1 9 PLIP interactions: 9 interactions with chain A Hydrophobic interactions: A:F.217, A:Y.342, A:Y.342 Hydrogen bonds: A:H.143, A:Y.342 pi-Stacking: A:H.189, A:Y.342 pi-Cation interactions: A:K.21, A:H.293

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.5: 10 residues within 4Å: Chain A: H.189, H.190, H.211, A.212, S.213, F.216, F.217, P.218, G.219, T.220 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:H.190, A:S.213, A:S.213, A:G.219

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Marek, M. et al., Characterization of Histone Deacetylase 8 (HDAC8) Selective Inhibition Reveals Specific Active Site Structural and Functional Determinants. J. Med. Chem. (2018)

Release Date

2018-10-31

Peptides

Histone deacetylase: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
D

Histone deacetylase

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