SMTL ID : 8g45.1

Structure of HDAC6 zinc-finger ubiquitin binding domain in complex with SGC-UBD253 chemical probe

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.62 Å

Oligo State

monomer

Ligands

3 x ZN: ZINC ION(Non-covalent)

ZN.1: 4 residues within 4Å: Chain A: C.39, C.42, H.58, H.64 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.39, A:C.42, A:H.58, A:H.64 ZN.2: 4 residues within 4Å: Chain A: C.27, C.30, C.47, H.54 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.27, A:C.30, A:C.47, A:H.54 ZN.3: 4 residues within 4Å: Chain A: C.7, H.9, C.77, C.80 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.7, A:H.9, A:C.77, A:C.80

1 x ZUE: 3-[8-chloro-3-(2-{[(2-methoxyphenyl)methyl]amino}-2-oxoethyl)-4-oxo-3,4-dihydroquinazolin-2-yl]propanoic acid(Non-covalent)

ZUE.4: 12 residues within 4Å: Chain A: E.35, W.37, G.48, R.49, L.56, S.69, I.71, D.72, S.74, W.76, Y.78, Y.83 13 PLIP interactions: 13 interactions with chain A Hydrophobic interactions: A:I.71, A:W.76, A:W.76, A:Y.78 Hydrogen bonds: A:R.49, A:R.49, A:L.56, A:Y.83 Water bridges: A:W.37 pi-Stacking: A:W.76, A:W.76 pi-Cation interactions: A:R.49, A:R.49

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Harding, R.J. et al., Discovery and Characterization of a Chemical Probe Targeting the Zinc-Finger Ubiquitin-Binding Domain of HDAC6. J.Med.Chem. (2023)

Release Date

2023-05-03

Peptides

Histone deacetylase 6: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Histone deacetylase 6

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