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

Crystal structure of Schistosoma mansoni HDAC8 complexed with an hydroxamate 4

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.07 Å

Oligo State

monomer

Ligands

1 x DMF: DIMETHYLFORMAMIDE(Non-covalent)

DMF.1: 6 residues within 4Å: Chain A: D.385, E.387, D.389, I.390, D.391, F.393 No protein-ligand interaction detected (PLIP)

1 x ZN: ZINC ION(Non-covalent)

ZN.2: 4 residues within 4Å: Chain A: D.187, H.189, D.286 Ligands: FGN.5 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Ligand interactions Metal complexes: A:D.187, A:D.187, A:H.189, A:D.286, FGN.5

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:V.209 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 FGN: (~{E})-3-[2-[[2,6-bis(chloranyl)phenyl]methoxy]phenyl]-~{N}-oxidanyl-prop-2-enamide(Non-covalent)

FGN.5: 12 residues within 4Å: Chain A: K.21, D.101, H.142, H.143, D.187, H.189, D.286, P.292, H.293, G.340, Y.342 Ligands: ZN.2 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:P.292, A:Y.342, A:Y.342 Hydrogen bonds: A:H.143 pi-Stacking: A:Y.342 pi-Cation interactions: A:K.21

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.6: 10 residues within 4Å: Chain A: H.190, E.195, T.220, G.221, T.222, N.224, I.233, F.234, L.235, N.247 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:E.195, A:G.221, A:T.222, A:T.222, A:I.233, A:L.235, A:N.247

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Bayer, T. et al., Synthesis, Crystallization Studies, and in vitro Characterization of Cinnamic Acid Derivatives as SmHDAC8 Inhibitors for the Treatment of Schistosomiasis. ChemMedChem (2018)

Release Date

2018-08-15

Peptides

Histone deacetylase: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
C

Histone deacetylase

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