SMTL ID : 6hsz.1

Crystal structure of Schistosoma mansoni HDAC8 complexed with a benzohydroxamate inhibitor 2

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.37 Å

Oligo State

homo-tetramer

Ligands

4 x ZN: ZINC ION(Non-covalent)

ZN.1: 5 residues within 4Å: Chain A: D.187, H.189, D.286, G.340 Ligands: GOW.4 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:D.187, A:D.187, A:H.189, A:D.286 ZN.7: 4 residues within 4Å: Chain B: D.187, H.189, D.286 Ligands: GOW.10 3 PLIP interactions: 3 interactions with chain B Metal complexes: B:D.187, B:H.189, B:D.286 ZN.13: 4 residues within 4Å: Chain C: D.187, H.189, D.286 Ligands: GOW.16 3 PLIP interactions: 3 interactions with chain C Metal complexes: C:D.187, C:H.189, C:D.286 ZN.18: 4 residues within 4Å: Chain D: D.187, H.189, D.286 Ligands: GOW.21 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:H.189, A:S.208, A:V.209 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.3 K.8: 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.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.14: 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:S.208 K.15: 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.9 K.19: 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.20: 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.12

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

GOW.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:P.292, A:Y.342 Hydrogen bonds: A:K.21, A:H.143, A:D.187, A:H.293 pi-Cation interactions: A:K.21 GOW.10: 14 residues within 4Å: Chain A: D.51 Chain B: 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.7 11 PLIP interactions: 11 interactions with chain B 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 GOW.16: 14 residues within 4Å: Chain C: K.21, 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.13 10 PLIP interactions: 9 interactions with chain C, 1 interactions with chain D Hydrophobic interactions: C:F.217, C:P.292, C:Y.342, C:Y.342, D:D.51 Hydrogen bonds: C:H.143, C:D.187, C:H.189, C:H.293 pi-Cation interactions: C:K.21 GOW.21: 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.18 9 PLIP interactions: 9 interactions with chain D Hydrophobic interactions: D:F.217, D:P.292, D:Y.342, D:Y.342 Hydrogen bonds: D:H.143, D:D.187, D:H.293, D:Y.342 pi-Cation interactions: D:K.21

7 x GOL: GLYCEROL(Non-functional Binders)

GOL.5: 11 residues within 4Å: Chain A: H.189, H.190, H.210, H.211, A.212, S.213, F.216, F.217, P.218, G.219, T.220 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:L.188, A:S.213, A:S.213, A:G.219, A:G.219 GOL.6: 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.11: 9 residues within 4Å: Chain B: H.190, E.195, W.199, 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:I.233, B:L.235, B:N.247 GOL.12: 4 residues within 4Å: Chain B: Y.36, K.37, M.367, T.368 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:K.37, B:T.368 GOL.17: 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 5 PLIP interactions: 5 interactions with chain C Hydrogen bonds: C:F.22, C:R.25, C:Y.26, C:Y.111, C:W.137 GOL.22: 9 residues within 4Å: Chain D: 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 D Hydrogen bonds: D:E.195, D:G.221, D:T.222, D:L.235, D:L.235, D:N.247 GOL.23: 8 residues within 4Å: Chain D: C.16, F.22, R.25, Y.26, Y.111, W.137, G.138, W.141 4 PLIP interactions: 4 interactions with chain D Hydrogen bonds: D:R.25, D:R.25, D:Y.111 Water bridges: D:Y.26

Links

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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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