SMTL ID : 8bjk.1

X-ray structure of Danio rerio histone deacetylase 6 (HDAC6) CD2 in complex with an inhibitor CPD11352

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.35 Å

Oligo State

monomer

Ligands

1 x ZN: ZINC ION(Non-covalent)

ZN.1: 4 residues within 4Å: Chain A: D.173, H.175, D.266 Ligands: QXF.4 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:D.173, A:D.173, A:H.175, A:D.266

2 x K: POTASSIUM ION(Non-covalent)

K.2: 6 residues within 4Å: Chain A: D.171, D.173, H.175, S.194, L.195, H.196 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:D.171, A:D.173, A:H.175, A:S.194, A:L.195 K.3: 4 residues within 4Å: Chain A: F.184, D.187, V.190, Y.223 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:F.184, A:D.187, A:V.190, A:Y.223, H2O.3

1 x QXF: ~{N}-[[5-(aminocarbamoyl)pyridin-2-yl]methyl]-~{N}-(3-chlorophenyl)methanesulfonamide(Non-covalent)

QXF.4: 14 residues within 4Å: Chain A: H.24, P.25, S.92, H.134, H.135, G.143, F.144, D.173, H.175, F.204, D.266, L.273, Y.306 Ligands: ZN.1 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:H.135, A:Y.306 Water bridges: A:F.204, A:F.204 pi-Stacking: A:F.144, A:F.144, A:H.175

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Motlova, L. et al., Comprehensive Mechanistic View of the Hydrolysis of Oxadiazole-Based Inhibitors by Histone Deacetylase 6 (HDAC6). Acs Chem.Biol. (2023)

Release Date

2023-09-06

Peptides

Histone deacetylase 6: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Histone deacetylase 6

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