SMTL ID : 6gx3.1

Crystal structure of Schistosoma mansoni HDAC8 complexed with an hydroxamate 1

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.10 Å

Oligo State

homo-tetramer

Ligands

4 x ZN: ZINC ION(Non-covalent)

ZN.1: 4 residues within 4Å: Chain A: D.187, H.189, D.286 Ligands: FF2.4 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:D.187, A:D.187, A:H.189, A:D.286 ZN.8: 4 residues within 4Å: Chain B: D.187, H.189, D.286 Ligands: FF2.11 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:D.187, B:D.187, B:H.189, B:D.286 ZN.16: 4 residues within 4Å: Chain C: D.187, H.189, D.286 Ligands: FF2.19 3 PLIP interactions: 3 interactions with chain C Metal complexes: C:D.187, C:H.189, C:D.286 ZN.24: 4 residues within 4Å: Chain D: D.187, H.189, D.286 Ligands: FF2.27 4 PLIP interactions: 4 interactions with chain D Metal complexes: D:D.187, D:D.187, D:H.189, D:D.286

8 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.2 K.9: 4 residues within 4Å: Chain B: F.198, S.201, V.204, S.244 5 PLIP interactions: 4 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:F.198, B:S.201, B:V.204, B:S.244, H2O.6 K.10: 7 residues within 4Å: Chain B: D.185, L.186, D.187, H.189, S.208, V.209, H.210 5 PLIP interactions: 5 interactions with chain B Metal complexes: B:D.185, B:D.185, B:D.187, B:H.189, B:S.208 K.17: 4 residues within 4Å: Chain C: F.198, S.201, V.204, S.244 5 PLIP interactions: 4 interactions with chain C, 1 Ligand-Water interactions Metal complexes: C:F.198, C:S.201, C:V.204, C:S.244, H2O.12 K.18: 7 residues within 4Å: Chain C: D.185, L.186, D.187, H.189, S.208, V.209, H.210 5 PLIP interactions: 5 interactions with chain C Metal complexes: C:D.185, C:D.185, C:D.187, C:H.189, C:V.209 K.25: 4 residues within 4Å: Chain D: F.198, S.201, V.204, S.244 5 PLIP interactions: 4 interactions with chain D, 1 Ligand-Water interactions Metal complexes: D:F.198, D:S.201, D:V.204, D:S.244, H2O.16 K.26: 7 residues within 4Å: Chain D: D.185, L.186, D.187, H.189, S.208, V.209, H.210 5 PLIP interactions: 5 interactions with chain D Metal complexes: D:D.185, D:D.185, D:D.187, D:H.189, D:V.209

8 x FF2: 4-chloranyl-~{N}-oxidanyl-1-benzothiophene-2-carboxamide(Non-covalent)

FF2.4: 12 residues within 4Å: Chain A: 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 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:F.217 Hydrogen bonds: A:H.143 FF2.5: 8 residues within 4Å: Chain A: E.132, V.133, L.328, K.331, V.332, P.333, E.361, V.362 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:V.133, A:K.331, A:V.362 Hydrogen bonds: A:V.362 FF2.11: 13 residues within 4Å: Chain A: D.51 Chain B: D.101, H.142, H.143, G.151, D.187, H.189, F.217, D.286, H.293, G.340, Y.342 Ligands: ZN.8 4 PLIP interactions: 4 interactions with chain B Hydrophobic interactions: B:F.217 Hydrogen bonds: B:H.143, B:D.187, B:Y.342 FF2.12: 8 residues within 4Å: Chain B: E.132, V.133, L.328, K.331, V.332, P.333, E.361, V.362 5 PLIP interactions: 5 interactions with chain B Hydrophobic interactions: B:E.132, B:V.133, B:L.328, B:V.362 Hydrogen bonds: B:V.362 FF2.19: 13 residues within 4Å: Chain C: D.101, H.142, H.143, G.151, D.187, H.189, F.217, D.286, H.293, G.340, Y.342 Chain D: D.51 Ligands: ZN.16 4 PLIP interactions: 4 interactions with chain C Hydrophobic interactions: C:F.217 Hydrogen bonds: C:H.143, C:D.187 pi-Stacking: C:H.189 FF2.20: 8 residues within 4Å: Chain C: E.132, V.133, L.328, K.331, V.332, P.333, E.361, V.362 5 PLIP interactions: 5 interactions with chain C Hydrophobic interactions: C:V.133, C:L.328, C:V.362 Hydrogen bonds: C:E.132, C:V.362 FF2.27: 13 residues within 4Å: Chain D: D.101, H.142, H.143, G.151, F.152, D.187, H.189, F.217, D.286, H.293, G.340, Y.342 Ligands: ZN.24 6 PLIP interactions: 6 interactions with chain D Hydrophobic interactions: D:F.152, D:F.152, D:F.217 Hydrogen bonds: D:H.143, D:D.187, D:Y.342 FF2.28: 7 residues within 4Å: Chain D: E.132, V.133, L.328, K.331, V.332, P.333, V.362 4 PLIP interactions: 4 interactions with chain D Hydrophobic interactions: D:V.133, D:K.331, D:V.362 Hydrogen bonds: D:E.132

6 x GOL: GLYCEROL(Non-functional Binders)

GOL.6: 8 residues within 4Å: Chain A: Y.111, S.112, A.115, W.141, F.152, C.153, Y.154, L.155 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:Y.111, A:Y.111, A:S.112, A:Y.154, A:L.155, A:L.155 GOL.7: 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:N.224, A:I.233, A:L.235 GOL.13: 6 residues within 4Å: Chain B: W.199, L.235, N.236, G.237, R.242, F.243 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:N.236, B:N.236, B:G.237 GOL.14: 8 residues within 4Å: Chain B: H.190, E.195, T.220, G.221, T.222, F.234, L.235, N.247 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:E.195, B:G.221, B:T.222, B:L.235, B:L.235, B:N.247 GOL.21: 8 residues within 4Å: Chain C: H.190, E.195, T.220, G.221, T.222, F.234, L.235, N.247 6 PLIP interactions: 6 interactions with chain C Hydrogen bonds: C:E.195, C:G.221, C:T.222, C:T.222, C:L.235, C:N.247 GOL.22: 7 residues within 4Å: Chain C: G.9, D.10, Q.11, Y.12, L.15, P.47, Q.117 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:Q.11, C:Y.12 Water bridges: C:Q.49, C:Q.117

2 x DMF: DIMETHYLFORMAMIDE(Non-covalent)

DMF.15: 7 residues within 4Å: Chain B: Y.302, R.353, A.356, L.357, E.360, M.367, I.369 No protein-ligand interaction detected (PLIP) DMF.23: 6 residues within 4Å: Chain C: Y.8, R.13, M.30, D.31, N.34, I.39 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:R.13

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Bayer, T. et al., Synthesis, Crystallization Studies, and in vitro Characterization of Cinnamic Acid Derivatives as SmHDAC8 Inhibitors for the Treatment of Schistosomiasis. ChemMedChem (2018)

Release Date

2018-08-15

Peptides

Histone deacetylase: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

Histone deacetylase

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