SMTL ID : 8d9a.2 (1 other biounit)

Crystal Structure of Danio rerio histone deacetylase 6 catalytic domain 2 complexed with fluorinated inhibitor 8

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.75 Å

Oligo State

monomer

Ligands

1 x QHO: 2,3,5-trifluoro-N-hydroxybenzamide(Non-covalent)

QHO.1: 12 residues within 4Å: Chain A: S.97, H.139, H.140, G.148, F.149, D.178, H.180, F.209, D.271, L.278, Y.311 Ligands: ZN.2 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:L.278 Hydrogen bonds: A:H.140 pi-Stacking: A:F.149, A:H.180, A:F.209 Halogen bonds: A:G.148

1 x ZN: ZINC ION(Non-covalent)

ZN.2: 4 residues within 4Å: Chain A: D.178, H.180, D.271 Ligands: QHO.1 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:D.178, A:D.178, A:H.180, A:D.271

2 x K: POTASSIUM ION(Non-covalent)

K.3: 6 residues within 4Å: Chain A: D.176, D.178, H.180, S.199, L.200, H.201 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:D.176, A:D.176, A:D.178, A:H.180, A:S.199 K.4: 4 residues within 4Å: Chain A: F.189, D.192, V.195, Y.228 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:F.189, A:D.192, A:V.195, A:Y.228, H2O.2

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Watson, P.R. et al., Aromatic Ring Fluorination Patterns Modulate Inhibitory Potency of Fluorophenylhydroxamates Complexed with Histone Deacetylase 6. Biochemistry (2022)

Release Date

2022-09-28

Peptides

Hdac6 protein: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

Hdac6 protein

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