SMTL ID : 8gd4.2 (1 other biounit)

Crystal Structure of Danio rerio histone deacetylase 6 catalytic domain 2 complexed with DMFO Inhibitor 6

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.00 Å

Oligo State

monomer

Ligands

1 x Z4I: 2-(benzylamino)-N'-(difluoroacetyl)pyrimidine-5-carbohydrazide(Non-covalent)

Z4I.1: 18 residues within 4Å: Chain A: H.29, P.30, S.97, P.137, H.139, H.140, G.148, F.149, C.150, D.178, H.180, F.209, D.271, L.278, E.308, G.309, Y.311 Ligands: ZN.2 9 PLIP interactions: 9 interactions with chain A Hydrophobic interactions: A:P.30, A:F.149, A:F.149, A:L.278 Hydrogen bonds: A:S.97, A:S.97, A:H.140 pi-Stacking: A:H.180, 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: Z4I.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.3: 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 K.4: 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

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Konig, B. et al., Difluoromethyl-1,3,4-oxadiazoles Are Selective, Mechanism-Based, and Essentially Irreversible Inhibitors of Histone Deacetylase 6. J.Med.Chem. (2023)

Release Date

2023-10-04

Peptides

Hdac6 protein: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

Hdac6 protein

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