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

Crystal structure of Danio rerio histone deacetylase 6 catalytic domain 2 in complex with DDK-137

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.20 Å

Oligo State

monomer

Ligands

1 x ZN: ZINC ION(Non-covalent)

ZN.1: 4 residues within 4Å: Chain A: D.178, H.180, D.271 Ligands: HB7.4 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.178, A:D.178, A:H.180, A:D.271, H2O.1

2 x K: POTASSIUM ION(Non-covalent)

K.2: 5 residues within 4Å: Chain A: D.176, D.178, H.180, S.199, L.200 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.3: 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.1

1 x HB7: N-[2-(benzylamino)-2-oxoethyl]-4-(dimethylamino)-N-{[4-(hydroxycarbamoyl)phenyl]methyl}benzamide(Non-covalent)

HB7.4: 15 residues within 4Å: Chain A: D.26, H.29, P.30, S.97, H.140, G.148, F.149, D.178, H.180, F.209, D.271, L.278, G.309, Y.311 Ligands: ZN.1 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:F.209 Hydrogen bonds: A:Y.311 Water bridges: A:S.97, A:F.209 pi-Stacking: A:F.149

1 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.5: 11 residues within 4Å: Chain A: V.179, H.180, H.181, H.201, R.202, Y.203, F.208, F.209, P.210, S.212, A.215 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:V.179, A:H.181, A:S.212

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Porter, N.J. et al., Histone Deacetylase 6-Selective Inhibitors and the Influence of Capping Groups on Hydroxamate-Zinc Denticity. J. Med. Chem. (2018)

Release Date

2018-08-29

Peptides

Hdac6 protein: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
D

Hdac6 protein

Related Entries With Identical Sequence