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

Crystal structure of Schistosoma mansoni HDAC8 complexed with a benzohydroxamate inhibitor 7

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.75 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: GQZ.4 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:D.187, 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 GQZ: ~{N}1-oxidanyl-~{N}3-phenyl-benzene-1,3-dicarboxamide(Non-covalent)

GQZ.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 10 PLIP interactions: 10 interactions with chain A Hydrophobic interactions: A:F.217, A:P.292, A:P.292, A:Y.342, A:Y.342, A:Y.342 Hydrogen bonds: A:K.21, A:H.143, A:H.293, A:Y.342

7 x DMF: DIMETHYLFORMAMIDE(Non-covalent)

DMF.5: 6 residues within 4Å: Chain A: Y.8, R.13, M.30, D.31, N.34, I.39 No protein-ligand interaction detected (PLIP) DMF.6: 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.7: 2 residues within 4Å: Chain A: E.196, W.199 1 PLIP interactions: 1 interactions with chain A Water bridges: A:K.145 DMF.8: 5 residues within 4Å: Chain A: I.254, D.258, D.403, S.404, I.405 No protein-ligand interaction detected (PLIP) DMF.9: 4 residues within 4Å: Chain A: Y.322, K.325, K.326, S.329 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:S.329 Water bridges: A:K.326 DMF.10: 7 residues within 4Å: Chain A: Y.302, R.353, A.356, L.357, E.360, M.367, I.369 1 PLIP interactions: 1 interactions with chain A Water bridges: A:Y.302 DMF.11: 1 residues within 4Å: Chain A: R.146 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:R.146

4 x GOL: GLYCEROL(Non-functional Binders)

GOL.12: 8 residues within 4Å: Chain A: H.190, E.195, T.220, G.221, T.222, 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:L.235, A:L.235, A:N.247 GOL.13: 6 residues within 4Å: Chain A: Q.11, Y.12, L.15, Q.49, A.114, Q.117 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Q.49, A:Q.117 GOL.14: 7 residues within 4Å: Chain A: A.212, T.222, W.223, P.249, L.250, E.251, H.408 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:A.212, A:T.222, A:L.250 GOL.15: 7 residues within 4Å: Chain A: Y.36, K.37, L.38, E.41, K.366, M.367, T.368 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:K.37, A:K.366, A:T.368, A:T.368

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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