SMTL ID : 6hu0.1 (3 other biounits)

Crystal structure of Schistosoma mansoni HDAC8 complexed with a benzohydroxamate inhibitor 9

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: T86.4 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.8

1 x T86: 3-[(2,4-dichlorophenyl)carbonylamino]-4-methoxy-~{N}-oxidanyl-benzamide(Non-covalent)

T86.4: 14 residues within 4Å: Chain A: K.21, D.101, 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 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:F.217, A:F.217, A:Y.342 Hydrogen bonds: A:K.21, A:H.143, A:H.293 pi-Cation interactions: A:K.21, A:H.293

3 x DMF: DIMETHYLFORMAMIDE(Non-covalent)

DMF.5: 2 residues within 4Å: Chain A: D.10, R.44 No protein-ligand interaction detected (PLIP) DMF.6: 6 residues within 4Å: Chain A: Y.8, R.13, M.30, D.31, N.34, I.39 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.13 Water bridges: A:N.34 DMF.7: 6 residues within 4Å: Chain A: Y.302, R.353, A.356, L.357, E.360, I.369 No protein-ligand interaction detected (PLIP)

8 x GOL: GLYCEROL(Non-functional Binders)

GOL.8: 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 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:L.235, A:N.247 Water bridges: A:N.224 GOL.9: 5 residues within 4Å: Chain A: R.13, Q.14, C.17, D.24, Y.378 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:R.13, A:Q.14 Water bridges: A:C.17, A:D.24, A:Y.378 GOL.10: 3 residues within 4Å: Chain A: D.94, S.95, S.97 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:S.97, A:S.97 Water bridges: A:S.95 GOL.11: 7 residues within 4Å: Chain A: E.132, V.133, L.328, K.331, V.332, P.333, V.362 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:K.331, A:V.332 Water bridges: A:W.330, A:K.331 GOL.12: 7 residues within 4Å: Chain A: Q.11, Y.12, L.15, P.47, Q.49, A.114, Q.117 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Q.49, A:Q.117 Water bridges: A:Q.11 GOL.13: 4 residues within 4Å: Chain A: Q.76, C.80, P.106, D.110 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Q.76 Water bridges: A:Q.76, A:Q.76 GOL.14: 7 residues within 4Å: Chain A: V.45, P.46, P.47, L.48, A.121, S.124, A.125 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:P.46, A:S.124, A:S.124, A:A.125 Water bridges: A:R.164 GOL.15: 7 residues within 4Å: Chain A: A.212, W.223, P.249, L.250, E.251, S.404, H.408 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:A.212, A:S.404, A:S.404, A:H.408 Water bridges: A:E.251

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
A

Histone deacetylase

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