SMTL ID : 6hu3.2 (3 other biounits)

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

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.65 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: GRZ.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.6

1 x GRZ: 1-[5-chloranyl-2-(4-fluoranylphenoxy)phenyl]-~{N}-oxidanyl-1,2,3-triazole-4-carboxamide(Non-covalent)

GRZ.4: 13 residues within 4Å: Chain A: 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.1 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:Y.342 Hydrogen bonds: A:H.143, A:Y.342 pi-Stacking: A:H.189

6 x DMF: DIMETHYLFORMAMIDE(Non-covalent)

DMF.5: 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.6: 5 residues within 4Å: Chain A: R.13, Q.14, C.17, D.24, Y.378 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:R.13 DMF.7: 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.8: 2 residues within 4Å: Chain A: E.196, W.199 No protein-ligand interaction detected (PLIP) DMF.9: 6 residues within 4Å: Chain A: Y.36, K.37, K.366, M.367, T.368, I.369 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:T.368 DMF.10: 2 residues within 4Å: Chain A: F.393, H.395 No protein-ligand interaction detected (PLIP)

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.11: 10 residues within 4Å: Chain A: H.190, E.195, W.199, T.220, G.221, T.222, I.233, 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:T.222, A:I.233, A:L.235, A:N.247

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
B

Histone deacetylase

Related Entries With Identical Sequence