SMTL ID : 6v79.1 (1 other biounit)

Crystal structure of Danio rerio histone deacetylase 6 catalytic domain 2 (CD2) complexed with NF2376

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.04 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: QQD.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: 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.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.2

1 x QQD: 4-{[(2S)-3,3-dimethyl-2-(pyridin-3-yl)-2,3-dihydro-1H-indol-1-yl]methyl}-N-hydroxybenzamide(Non-covalent)

QQD.4: 13 residues within 4Å: Chain A: S.97, H.140, G.148, F.149, D.178, H.180, F.209, N.211, D.271, L.278, G.309, Y.311 Ligands: ZN.1 9 PLIP interactions: 9 interactions with chain A Hydrophobic interactions: A:F.149, A:F.209, A:F.209, A:L.278 Hydrogen bonds: A:H.180, A:N.211, A:G.310 pi-Stacking: A:F.149, A:F.209

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

EDO.5: 2 residues within 4Å: Chain A: S.50, C.52 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Campiani, G. et al., Harnessing the Role of HDAC6 in Idiopathic Pulmonary Fibrosis: Design, Synthesis, Structural Analysis, and Biological Evaluation of Potent Inhibitors. J.Med.Chem. (2021)

Release Date

2020-12-02

Peptides

Hdac6 protein: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Hdac6 protein

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