SMTL ID : 8g20.1 (1 other biounit)

Crystal Structure of Danio rerio histone deacetylase 6 catalytic domain 2 complexed with inhibitor Mz327

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.77 Å

Oligo State

monomer

Ligands

1 x YJ5: 4-[(N-butylpentanamido)methyl]-N-hydroxybenzamide(Non-covalent)

YJ5.1: 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, D.271, L.278, Y.311 Ligands: EDO.2, ZN.5 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:P.30, A:F.149, A:F.149, A:F.149 Hydrogen bonds: A:H.140 Water bridges: A:F.209 pi-Stacking: A:H.180, A:F.209

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

EDO.2: 7 residues within 4Å: Chain A: N.23, H.29, S.97, I.98, F.99, F.149 Ligands: YJ5.1 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.23 Water bridges: A:I.98 EDO.3: 4 residues within 4Å: Chain A: L.123, T.166, L.170, R.302 5 PLIP interactions: 5 interactions with chain A Water bridges: A:L.123, A:L.123, A:E.262, A:R.302, A:R.302 EDO.4: 3 residues within 4Å: Chain A: G.275, D.276, P.277 No protein-ligand interaction detected (PLIP)

1 x ZN: ZINC ION(Non-covalent)

ZN.5: 4 residues within 4Å: Chain A: D.178, H.180, D.271 Ligands: YJ5.1 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.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.3, H2O.5 K.7: 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

1 x EOH: ETHANOL(Non-functional Binders)

EOH.8: 2 residues within 4Å: Chain A: P.30, P.277 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:P.30

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Sinatra, L. et al., Development of First-in-Class Dual Sirt2/HDAC6 Inhibitors as Molecular Tools for Dual Inhibition of Tubulin Deacetylation. J.Med.Chem. (2023)

Release Date

2023-12-13

Peptides

Hdac6 protein: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Hdac6 protein

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