SMTL ID : 8g1z.1

Crystal Structure of Danio rerio histone deacetylase 6 catalytic domain 2 complexed with inhibitor Mz317

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.87 Å

Oligo State

monomer

Ligands

1 x YIZ: 4-(acetamidomethyl)-N-hydroxybenzamide(Non-covalent)

YIZ.1: 12 residues within 4Å: Chain A: S.97, H.140, G.148, F.149, D.178, H.180, F.209, D.271, G.309, Y.311 Ligands: ZN.2, EDO.6 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:S.97, A:H.180, A:Y.311 pi-Stacking: A:F.149, A:F.209

1 x ZN: ZINC ION(Non-covalent)

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

2 x K: POTASSIUM ION(Non-covalent)

K.3: 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.178, A:H.180, A:S.199, A:L.200 K.4: 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.2, H2O.5

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

EDO.5: 4 residues within 4Å: Chain A: A.260, P.261, L.298, A.299 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:A.299 EDO.6: 5 residues within 4Å: Chain A: H.180, F.208, F.209, L.278 Ligands: YIZ.1 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:F.209, A:L.278 EDO.7: 3 residues within 4Å: Chain A: D.205, N.216, Y.217 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:D.205, A:D.205, A:N.216 Water bridges: A:N.235

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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