SMTL ID : 6htz.2 (3 other biounits)

Crystal structure of Schistosoma mansoni HDAC8 complexed with a benzohydroxamate inhibitor 8

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.84 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: GRK.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:S.208 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.7

1 x GRK: 4-methoxy-~{N}-oxidanyl-3-(2-phenylethanoylamino)benzamide(Non-covalent)

GRK.4: 13 residues within 4Å: Chain A: K.21, D.101, H.142, H.143, G.151, D.187, H.189, F.217, D.286, H.293, G.340, Y.342 Ligands: ZN.1 9 PLIP interactions: 9 interactions with chain A Hydrophobic interactions: A:F.217, A:F.217, A:Y.342 Hydrogen bonds: A:K.21, A:H.143, A:D.187, A:H.293, A:Y.342 pi-Cation interactions: A:K.21

9 x DMF: DIMETHYLFORMAMIDE(Non-covalent)

DMF.5: 7 residues within 4Å: Chain A: Y.302, R.353, A.356, L.357, E.360, M.367, I.369 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.353, A:I.369 DMF.6: 5 residues within 4Å: Chain A: Y.8, M.30, D.31, N.34, I.39 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.13, A:D.31 DMF.7: 4 residues within 4Å: Chain A: R.13, Q.14, C.17, Y.378 1 PLIP interactions: 1 interactions with chain A Water bridges: A:R.13 DMF.8: 6 residues within 4Å: Chain A: Q.11, Y.12, L.15, P.47, Q.49, Q.117 1 PLIP interactions: 1 interactions with chain A Water bridges: A:Q.117 DMF.9: 5 residues within 4Å: Chain A: Y.36, K.37, K.366, M.367, T.368 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:T.368 DMF.10: 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 Hydrogen bonds: A:K.331 DMF.11: 1 residues within 4Å: Chain A: W.199 1 PLIP interactions: 1 interactions with chain A Water bridges: A:E.196 DMF.12: 4 residues within 4Å: Chain A: I.254, D.403, S.404, I.405 No protein-ligand interaction detected (PLIP) DMF.13: 3 residues within 4Å: Chain A: K.325, K.326, S.329 1 PLIP interactions: 1 interactions with chain A Water bridges: A:K.326

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.14: 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

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
B

Histone deacetylase

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