SMTL ID : 6htt.3 (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 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.9

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 9 PLIP interactions: 9 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

8 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 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:R.13 DMF.6: 4 residues within 4Å: Chain A: R.13, Q.14, C.17, Y.378 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.13, A:Q.14 DMF.7: 2 residues within 4Å: Chain A: E.196, W.199 No protein-ligand interaction detected (PLIP) DMF.8: 6 residues within 4Å: Chain A: A.62, F.63, H.163, A.197, F.198 Ligands: DMF.12 No protein-ligand interaction detected (PLIP) DMF.9: 4 residues within 4Å: Chain A: I.254, D.258, D.403, S.404 1 PLIP interactions: 1 interactions with chain A Water bridges: A:E.251 DMF.10: 1 residues within 4Å: Chain A: E.375 No protein-ligand interaction detected (PLIP) DMF.11: 3 residues within 4Å: Chain A: K.325, K.326, S.329 No protein-ligand interaction detected (PLIP) DMF.12: 5 residues within 4Å: Chain A: F.63, R.146, E.196, A.197 Ligands: DMF.8 No protein-ligand interaction detected (PLIP)

7 x GOL: GLYCEROL(Non-functional Binders)

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.11, A:Q.117 GOL.14: 6 residues within 4Å: Chain A: E.132, V.133, L.328, K.331, V.332, V.362 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:K.331, A:K.331, A:K.331 Water bridges: A:V.332 GOL.15: 8 residues within 4Å: Chain A: H.190, E.195, T.220, G.221, T.222, F.234, L.235, N.247 8 PLIP interactions: 8 interactions with chain A Hydrogen bonds: A:E.195, A:G.221, A:T.222, A:T.222, A:L.235, A:N.247 Water bridges: A:N.224, A:N.224 GOL.16: 7 residues within 4Å: Chain A: A.212, T.222, W.223, P.249, L.250, E.251, H.408 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:A.212, A:T.222, A:T.222, A:L.250 GOL.17: 7 residues within 4Å: Chain A: Y.302, R.353, A.356, L.357, E.360, M.367, I.369 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.353, A:E.360 Water bridges: A:I.369 GOL.18: 7 residues within 4Å: Chain A: Y.36, K.37, L.38, E.41, K.366, M.367, T.368 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:K.37, A:E.41, A:K.366, A:T.368, A:T.368 Water bridges: A:T.368 GOL.19: 4 residues within 4Å: Chain A: R.410, S.443, L.444, P.446 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.410, A:L.444

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
C

Histone deacetylase

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