SMTL ID : 6zw1.1

X-ray structure of Danio rerio histone deacetylase 6 (HDAC6) CD2 in complex with an inhibitor SW101

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.13 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: QRB.2 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:D.173, A:D.173, A:H.175, A:D.266

1 x QRB: 1-[[4-(oxidanylcarbamoyl)phenyl]methyl]-3,4-dihydro-2~{H}-quinoline-6-carboxamide(Non-covalent)

QRB.2: 14 residues within 4Å: Chain A: 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, SCN.7 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:F.144, A:L.273 Hydrogen bonds: A:H.135 Water bridges: A:H.23 pi-Stacking: A:F.144, A:F.204

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.3: 3 residues within 4Å: Chain A: R.162, R.166, E.257 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.166, A:R.166 Water bridges: A:R.162 GOL.4: 3 residues within 4Å: Chain A: A.202, N.206 Ligands: SCN.7 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.206, A:N.206

2 x K: POTASSIUM ION(Non-covalent)

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

2 x SCN: THIOCYANATE ION(Non-functional Binders)

SCN.7: 4 residues within 4Å: Chain A: F.203, F.204 Ligands: QRB.2, GOL.4 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:F.204 SCN.8: 7 residues within 4Å: Chain A: Q.181, E.185, K.214, V.215, G.216, L.217, N.224 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:V.215, A:G.216

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Shen, S. et al., Tetrahydroquinoline-Capped Histone Deacetylase 6 Inhibitor SW-101 Ameliorates Pathological Phenotypes in a Charcot-Marie-Tooth Type 2A Mouse Model. J.Med.Chem. (2021)

Release Date

2021-08-04

Peptides

Histone deacetylase 6: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Histone deacetylase 6

Related Entries With Identical Sequence