SMTL ID : 6hti.3 (3 other biounits)

Crystal structure of Schistosoma mansoni HDAC8 complexed with a benzohydroxamate inhibitor 6

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.69 Å

Oligo State

monomer

Ligands

1 x GQW: ~{N}-[2-chloranyl-5-(oxidanylcarbamoyl)phenyl]-1-benzothiophene-7-carboxamide(Non-covalent)

GQW.1: 13 residues within 4Å: Chain A: K.21, H.142, H.143, G.151, D.187, H.189, F.217, D.286, P.292, H.293, G.340, Y.342 Ligands: ZN.2 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:F.217, A:P.292, A:P.292, A:Y.342 Hydrogen bonds: A:K.21, A:H.143, A:H.293 pi-Cation interactions: A:K.21

1 x ZN: ZINC ION(Non-covalent)

ZN.2: 4 residues within 4Å: Chain A: D.187, H.189, D.286 Ligands: GQW.1 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Ligand interactions Metal complexes: A:D.187, A:H.189, A:D.286, GQW.1

2 x K: POTASSIUM ION(Non-covalent)

K.3: 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:S.208 K.4: 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.4

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.5: 9 residues within 4Å: Chain A: H.190, E.195, W.199, T.220, G.221, T.222, F.234, L.235, N.247 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:E.195, A:G.221, A:T.222, A:L.235, A:L.235, A:N.247

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
C

Histone deacetylase

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