SMTL ID : 6tld.4 (3 other biounits)

Crystal structure of Schistosoma mansoni HDAC8 complexed with a triazole hydroxamate inhibitor 2

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.61 Å

Oligo State

monomer

Ligands

8 x DMF: DIMETHYLFORMAMIDE(Non-covalent)

DMF.1: 1 residues within 4Å: Chain A: D.88 No protein-ligand interaction detected (PLIP) DMF.6: 4 residues within 4Å: Chain A: A.62, F.63, H.163, A.197 No protein-ligand interaction detected (PLIP) DMF.7: 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, A:D.31 DMF.8: 4 residues within 4Å: Chain A: R.13, Q.14, C.17, D.24 1 PLIP interactions: 1 interactions with chain A Water bridges: A:Y.378 DMF.9: 2 residues within 4Å: Chain A: E.196, W.199 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: 6 residues within 4Å: Chain A: Y.8, I.39, P.40, L.42, S.43, R.44 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.44 Water bridges: A:Y.8 DMF.12: 3 residues within 4Å: Chain A: K.21, P.292, H.293 No protein-ligand interaction detected (PLIP)

1 x ZN: ZINC ION(Non-covalent)

ZN.2: 4 residues within 4Å: Chain A: D.187, H.189, D.286 Ligands: NK5.5 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: 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.4: 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

1 x NK5: ~{N}-oxidanyl-1-phenyl-1,2,3-triazole-4-carboxamide(Non-covalent)

NK5.5: 10 residues within 4Å: Chain A: D.101, H.142, H.143, G.151, D.187, H.189, F.217, D.286, Y.342 Ligands: ZN.2 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:F.217, A:F.217 Hydrogen bonds: A:H.143, A:Y.342 pi-Stacking: A:H.189, A:F.217

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.13: 9 residues within 4Å: Chain A: H.190, E.195, T.220, G.221, T.222, N.224, 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:N.224, A:L.235, A:L.235, A:N.247

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Kalinin, D.V. et al., Structure-Based Design, Synthesis, and Biological Evaluation of Triazole-Based smHDAC8 Inhibitors. Chemmedchem (2020)

Release Date

2019-12-18

Peptides

Histone deacetylase: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
D

Histone deacetylase

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