SMTL ID : 7jom.2 (1 other biounit)

Crystal structure of Danio rerio histone deacetylase 6 catalytic domain 2 complexed with TO-317

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.84 Å

Oligo State

monomer

Ligands

1 x TO3: N-hydroxy-4-({[(pyridin-3-yl)methyl][(2,3,4,5-tetrafluorophenyl)sulfonyl]amino}methyl)benzamide(Non-covalent)

TO3.1: 14 residues within 4Å: Chain A: S.97, H.140, G.148, F.149, D.178, H.180, F.208, F.209, D.271, L.278, G.309, G.310, Y.311 Ligands: ZN.4 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:F.209, A:F.209, A:L.278 Hydrogen bonds: A:G.310 pi-Stacking: A:F.149

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

EDO.2: 4 residues within 4Å: Chain A: Q.186, H.187, E.190, D.214 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:Q.186, A:H.187 Water bridges: A:E.190, A:E.190

1 x FMT: FORMIC ACID(Non-functional Binders)

FMT.3: 3 residues within 4Å: Chain A: N.23, D.26, H.29 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.23, A:D.26

1 x ZN: ZINC ION(Non-covalent)

ZN.4: 4 residues within 4Å: Chain A: D.178, H.180, D.271 Ligands: TO3.1 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.2

2 x K: POTASSIUM ION(Non-covalent)

K.5: 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.3 K.6: 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.178, A:H.180, A:S.199, A:L.200

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Olaoye, O.O. et al., Unique Molecular Interaction with the Histone Deacetylase 6 Catalytic Tunnel: Crystallographic and Biological Characterization of a Model Chemotype. J.Med.Chem. (2021)

Release Date

2021-06-16

Peptides

Hdac6 protein: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

Hdac6 protein

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