SMTL ID : 6cea.1

Crystal structure of fragment 3-(quinolin-2-yl)propanoic acid bound in the ubiquitin binding pocket of the HDAC6 zinc-finger domain

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.60 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

3 x UNX: UNKNOWN ATOM OR ION(Non-functional Binders)

UNX.4: 1 residues within 4Å: Chain A: W.6 No protein-ligand interaction detected (PLIP) UNX.6: 3 residues within 4Å: Chain A: Y.46, H.58, N.61 No protein-ligand interaction detected (PLIP) UNX.7: 3 residues within 4Å: Chain A: P.5, H.85, H.86 No protein-ligand interaction detected (PLIP)

1 x EYY: 3-(quinolin-2-yl)propanoic acid(Non-covalent)

EYY.5: 7 residues within 4Å: Chain A: W.37, G.48, R.49, L.56, W.76, Y.78, Y.83 15 PLIP interactions: 15 interactions with chain A Hydrophobic interactions: A:W.37, A:W.37, A:W.76, A:W.76, A:Y.78 Hydrogen bonds: A:W.37, A:R.49, A:L.56 Water bridges: A:R.49 Salt bridges: A:R.49 pi-Stacking: A:W.76, 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

Ferreira de Freitas, R. et al., Identification and Structure-Activity Relationship of HDAC6 Zinc-Finger Ubiquitin Binding Domain Inhibitors. J. Med. Chem. (2018)

Release Date

2018-02-28

Peptides

Histone deacetylase 6: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Histone deacetylase 6

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