SMTL ID : 6hu1.4 (3 other biounits)

Crystal structure of Schistosoma mansoni HDAC8 complexed with a benzohydroxamate inhibitor 10

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.00 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: GT2.4 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: 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.5 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

1 x GT2: 4-chloranyl-3-[(2,4-dichlorophenyl)carbonylamino]-~{N}-oxidanyl-benzamide(Non-covalent)

GT2.4: 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.1 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:F.217, A:F.217 Hydrogen bonds: A:K.21, A:H.143, A:D.187, A:Y.342 Water bridges: A:H.293

8 x DMF: DIMETHYLFORMAMIDE(Non-covalent)

DMF.5: 4 residues within 4Å: Chain A: D.94, S.95, S.97, E.148 No protein-ligand interaction detected (PLIP) DMF.6: 5 residues within 4Å: Chain A: Y.8, R.13, M.30, D.31, N.34 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:R.13 DMF.7: 8 residues within 4Å: Chain A: C.16, F.22, R.25, Y.26, Y.111, W.137, G.138, W.141 No protein-ligand interaction detected (PLIP) DMF.8: 6 residues within 4Å: Chain A: E.132, V.133, K.331, V.332, P.333, V.362 1 PLIP interactions: 1 interactions with chain A Water bridges: A:K.331 DMF.9: 2 residues within 4Å: Chain A: E.196, W.199 No protein-ligand interaction detected (PLIP) DMF.10: 3 residues within 4Å: Chain A: R.13, Q.14, Y.378 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:R.13 DMF.11: 7 residues within 4Å: Chain A: L.75, H.79, L.85, M.93, L.98, P.103, G.104 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:G.104 DMF.12: 6 residues within 4Å: Chain A: Y.302, R.353, A.356, L.357, E.360, M.367 No protein-ligand interaction detected (PLIP)

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.13: 9 residues within 4Å: Chain A: H.190, E.195, T.220, G.221, T.222, N.224, 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:N.224, A:L.235, A:L.235, A:N.247 GOL.14: 5 residues within 4Å: Chain A: Q.11, L.15, P.47, Q.49, Q.117 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Q.117 Water bridges: A:Y.12, A:Q.49

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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