SMTL ID : 6pye.1 (1 other biounit)

Crystal structure of Danio rerio histone deacetylase 6 catalytic domain 2 complexed with NR160

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.48 Å

Oligo State

monomer

Ligands

1 x P5Y: N-[(1-benzyl-1H-tetrazol-5-yl)methyl]-N-{[4-(hydroxycarbamoyl)phenyl]methyl}-2-(trifluoromethyl)benzamide(Non-covalent)

P5Y.1: 15 residues within 4Å: Chain A: H.29, P.30, S.97, H.139, H.140, G.148, F.149, D.178, H.180, F.209, N.211, D.271, L.278, Y.311 Ligands: ZN.4 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:P.30, A:F.209, A:L.278 Hydrogen bonds: A:H.140, A:Y.311 pi-Stacking: A:F.149

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

EDO.2: 4 residues within 4Å: Chain A: Q.34, S.37, R.38, S.41 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:S.37, A:S.41, A:S.41 EDO.3: 3 residues within 4Å: Chain A: Y.14, F.40, R.54 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:R.54, A:R.54 Water bridges: A:Y.14, A:Y.14

1 x ZN: ZINC ION(Non-covalent)

ZN.4: 4 residues within 4Å: Chain A: D.178, H.180, D.271 Ligands: P5Y.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.5: 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.6: 4 residues within 4Å: Chain A: F.189, D.192, V.195, Y.228 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.192, A:V.195, A:Y.228, H2O.5, H2O.7

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Ressing, N. et al., Multicomponent Synthesis, Binding Mode, and Structure-Activity Relationship of Selective Histone Deacetylase 6 (HDAC6) Inhibitors with Bifurcated Capping Groups. J.Med.Chem. (2020)

Release Date

2020-07-29

Peptides

Hdac6 protein: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Hdac6 protein

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