SMTL ID : 6hsh.3 (3 other biounits)

Crystal structure of Schistosoma mansoni HDAC8 complexed with Quisinostat

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.54 Å

Oligo State

monomer

Ligands

9 x DMF: DIMETHYLFORMAMIDE(Non-covalent)

DMF.1: 5 residues within 4Å: Chain A: Y.36, K.37, K.366, M.367, T.368 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:T.368 Water bridges: A:T.368 DMF.7: 4 residues within 4Å: Chain A: R.13, C.17, A.27, Y.378 No protein-ligand interaction detected (PLIP) DMF.8: 2 residues within 4Å: Chain A: Y.8, R.44 No protein-ligand interaction detected (PLIP) DMF.9: 2 residues within 4Å: Chain A: S.377, Y.378 No protein-ligand interaction detected (PLIP) DMF.10: 7 residues within 4Å: Chain A: Y.302, R.353, A.356, L.357, E.360, M.367, I.369 No protein-ligand interaction detected (PLIP) DMF.11: 4 residues within 4Å: Chain A: R.410, S.443, L.444, P.446 No protein-ligand interaction detected (PLIP) DMF.12: 9 residues within 4Å: Chain A: S.19, P.20, K.21, F.22, D.101, F.105, Y.111, F.152, Y.154 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Y.111 DMF.13: 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.14: 3 residues within 4Å: Chain A: L.91, D.94, S.95 1 PLIP interactions: 1 interactions with chain A Water bridges: A:S.97

1 x ZN: ZINC ION(Non-covalent)

ZN.2: 4 residues within 4Å: Chain A: D.187, H.189, D.286 Ligands: GOK.5 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: 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.6 K.4: 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

2 x GOK: 2-[4-[[(1-methylindol-3-yl)methylamino]methyl]piperidin-1-yl]-~{N}-oxidanyl-pyrimidine-5-carboxamide(Non-covalent)

GOK.5: 13 residues within 4Å: Chain A: Y.100, D.101, H.142, H.143, G.151, F.152, D.187, H.189, F.217, D.286, H.293, Y.342 Ligands: ZN.2 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:D.101, A:H.143 Water bridges: A:G.340 pi-Stacking: A:F.152 GOK.6: 7 residues within 4Å: Chain A: E.195, E.196, W.199, G.219, T.220, N.224, M.225 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:E.196, A:W.199, A:N.224 Hydrogen bonds: A:G.219, A:N.224, A:M.225 pi-Stacking: A:W.199, A:W.199

3 x GOL: GLYCEROL(Non-functional Binders)

GOL.15: 6 residues within 4Å: Chain A: Q.11, Y.12, L.15, P.47, Q.49, Q.117 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Q.49, A:Q.117 Water bridges: A:Y.12 GOL.16: 5 residues within 4Å: Chain A: N.271, Q.275, P.276, W.330, V.332 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:N.271, A:Q.275, A:Q.275, A:W.330 GOL.17: 11 residues within 4Å: Chain A: H.190, E.195, W.199, T.220, G.221, T.222, N.224, I.233, 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: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
C

Histone deacetylase

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