SMTL ID : 6ht8.1

Crystal structure of Schistosoma mansoni HDAC8 complexed with a benzohydroxamate inhibitor 3

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.50 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: GQE.4 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:D.187, A:H.189, A:D.286 ZN.10: 4 residues within 4Å: Chain B: D.187, H.189, D.286 Ligands: GQE.13 3 PLIP interactions: 3 interactions with chain B Metal complexes: B:D.187, B:H.189, B:D.286 ZN.20: 4 residues within 4Å: Chain C: D.187, H.189, D.286 Ligands: GQE.23 3 PLIP interactions: 3 interactions with chain C Metal complexes: C:D.187, C:H.189, C:D.286 ZN.27: 4 residues within 4Å: Chain D: D.187, H.189, D.286 Ligands: GQE.30 3 PLIP interactions: 3 interactions with chain D Metal complexes: 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.11: 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:V.209 K.12: 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.8 K.21: 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.22: 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.28: 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:S.208 K.29: 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.17

4 x GQE: 3-benzamido-4-methoxy-~{N}-oxidanyl-benzamide(Non-covalent)

GQE.4: 13 residues within 4Å: Chain A: K.21, 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 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:F.217, A:F.217 Hydrogen bonds: A:K.21, A:H.143, A:D.187, A:H.293 pi-Cation interactions: A:K.21 GQE.13: 15 residues within 4Å: Chain A: D.51 Chain B: 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.10 12 PLIP interactions: 11 interactions with chain B, 1 interactions with chain A Hydrophobic interactions: B:F.217, B:F.217, B:P.292, B:Y.342, B:Y.342 Hydrogen bonds: B:K.21, B:H.143, B:D.187, B:H.293, B:Y.342 pi-Cation interactions: B:K.21 Water bridges: A:D.51 GQE.23: 15 residues within 4Å: Chain C: 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 Chain D: D.51 Ligands: ZN.20 11 PLIP interactions: 11 interactions with chain C Hydrophobic interactions: C:F.217, C:F.217, C:P.292, C:Y.342 Hydrogen bonds: C:K.21, C:H.143, C:D.187, C:H.293 Water bridges: C:G.340, C:G.340 pi-Cation interactions: C:K.21 GQE.30: 14 residues within 4Å: Chain D: 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.27 11 PLIP interactions: 11 interactions with chain D Hydrophobic interactions: D:F.217, D:F.217, D:P.292, D:Y.342, D:Y.342 Hydrogen bonds: D:K.21, D:H.143, D:D.187, D:H.293, D:Y.342 pi-Cation interactions: D:K.21

8 x GOL: GLYCEROL(Non-functional Binders)

GOL.5: 10 residues within 4Å: Chain A: H.189, H.190, H.211, A.212, S.213, F.216, F.217, P.218, G.219, T.220 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:L.188, A:H.190, A:S.213, A:S.213, A:G.219, A:G.219 GOL.6: 8 residues within 4Å: Chain A: C.16, F.22, R.25, Y.26, Y.111, W.137, G.138, W.141 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:R.25 GOL.7: 9 residues within 4Å: Chain A: H.190, E.195, T.220, G.221, T.222, N.224, 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:L.235, A:L.235, A:N.247 GOL.14: 8 residues within 4Å: Chain B: H.190, E.195, T.220, G.221, T.222, F.234, L.235, N.247 7 PLIP interactions: 7 interactions with chain B Hydrogen bonds: B:E.195, B:G.221, B:T.222, B:T.222, B:L.235, B:L.235, B:N.247 GOL.15: 10 residues within 4Å: Chain B: C.16, F.22, G.23, D.24, R.25, Y.26, Y.111, W.137, W.141, W.351 7 PLIP interactions: 7 interactions with chain B Hydrogen bonds: B:C.16, B:F.22, B:R.25, B:Y.26, B:Y.111, B:W.137 Water bridges: B:F.22 GOL.16: 4 residues within 4Å: Chain B: Y.302, R.353, I.369 Ligands: DMF.19 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:R.353, B:I.369 GOL.17: 8 residues within 4Å: Chain B: D.346, R.349, Y.382, G.383, P.384, D.385, I.390, D.391 9 PLIP interactions: 9 interactions with chain B Hydrogen bonds: B:R.349, B:R.349, B:D.385, B:D.391 Water bridges: B:T.290, B:N.343, B:N.343, B:N.343, B:G.383 GOL.24: 11 residues within 4Å: Chain C: C.16, C.17, F.22, G.23, D.24, R.25, Y.26, Y.111, W.137, G.138, W.141 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:G.23, C:R.25, C:Y.26, C:W.137

8 x DMF: DIMETHYLFORMAMIDE(Non-covalent)

DMF.8: 4 residues within 4Å: Chain A: R.13, Q.14, C.17, Y.378 No protein-ligand interaction detected (PLIP) DMF.9: 4 residues within 4Å: Chain A: D.94, S.95, S.97, E.148 1 PLIP interactions: 1 interactions with chain A Water bridges: A:S.97 DMF.18: 5 residues within 4Å: Chain B: Y.8, M.30, D.31, N.34, I.39 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:D.31 DMF.19: 7 residues within 4Å: Chain B: Y.302, R.353, A.356, L.357, M.367, I.369 Ligands: GOL.16 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:R.353, B:I.369 DMF.25: 6 residues within 4Å: Chain C: E.132, V.133, L.328, K.331, V.332, V.362 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:K.331 DMF.26: 6 residues within 4Å: Chain C: Y.302, R.353, A.356, L.357, E.360, M.367 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:I.369 DMF.31: 4 residues within 4Å: Chain D: R.13, C.17, A.27, Y.378 1 PLIP interactions: 1 interactions with chain D Water bridges: D:Y.378 DMF.32: 6 residues within 4Å: Chain C: Y.100 Chain D: P.46, L.48, A.121, S.124, A.125 1 PLIP interactions: 1 interactions with chain D Water bridges: D:Q.49

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: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

Histone deacetylase

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