SMTL ID : 8a8z.1 (1 other biounit)

Crystal structure of Danio rerio HDAC6 CD2 in complex with in situ enzymatically hydrolyzed DFMO-based ITF5924

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.60 Å

Oligo State

monomer

Ligands

1 x LDL: 4-[[4-[4-(imidazolidin-2-ylideneamino)phenyl]-1,2,3-triazol-1-yl]methyl]benzohydrazide(Non-covalent)

LDL.1: 16 residues within 4Å: Chain A: D.27, H.29, H.30, P.31, S.98, H.140, H.141, G.149, F.150, D.179, H.181, F.210, D.272, L.279, Y.312 Ligands: ZN.2 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:P.31, A:F.210, A:L.279 Hydrogen bonds: A:D.27, A:H.141, A:Y.312 Water bridges: A:Y.312 pi-Stacking: A:F.150

1 x ZN: ZINC ION(Non-covalent)

ZN.2: 4 residues within 4Å: Chain A: D.179, H.181, D.272 Ligands: LDL.1 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:D.179, A:D.179, A:H.181, A:D.272

2 x K: POTASSIUM ION(Non-covalent)

K.3: 4 residues within 4Å: Chain A: F.190, D.193, V.196, Y.229 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:F.190, A:D.193, A:V.196, A:Y.229, H2O.6 K.4: 5 residues within 4Å: Chain A: D.177, D.179, H.181, S.200, L.201 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:D.177, A:D.179, A:H.181, A:S.200, A:L.201

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Cellupica, E. et al., Difluoromethyl-1,3,4-oxadiazoles are slow-binding substrate analog inhibitors of histone deacetylase 6 with unprecedented isotype selectivity. J.Biol.Chem. (2022)

Release Date

2023-01-25

Peptides

Histone deacetylase 6: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Histone deacetylase 6

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