SMTL ID : 7p3s.4 (3 other biounits)

Crystal structure of Schistosoma mansoni HDAC8 complexed with a benzohydroxamate inhibitor 12

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.55 Å

Oligo State

monomer

Ligands

1 x 5IB: ~{N}-[2-methoxy-5-(oxidanylcarbamoyl)phenyl]dibenzofuran-4-carboxamide(Non-covalent)

5IB.1: 14 residues within 4Å: Chain A: K.21, D.101, 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 10 PLIP interactions: 10 interactions with chain A Hydrophobic interactions: A:F.217, A:F.217, A:P.292, A:Y.342, A:Y.342 Hydrogen bonds: A:K.21, A:H.143, A:D.187, A:Y.342 pi-Stacking: A:H.189

1 x ZN: ZINC ION(Non-covalent)

ZN.2: 4 residues within 4Å: Chain A: D.187, H.189, D.286 Ligands: 5IB.1 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.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.7

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.5: 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 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:E.195, A:G.221, A:T.222, A:I.233, A:L.235, A:N.247 GOL.6: 6 residues within 4Å: Chain A: Q.11, Y.12, L.15, P.47, Q.49, Q.117 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:Q.11, A:Q.117 Water bridges: A:Q.11, A:Y.12

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Ghazy, E. et al., Synthesis, structure-activity relationships, cocrystallization and cellular characterization of novel smHDAC8 inhibitors for the treatment of schistosomiasis. Eur.J.Med.Chem. (2021)

Release Date

2021-09-15

Peptides

Histone deacetylase: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
D

Histone deacetylase

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