SMTL ID : 5wpb.1

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

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.55 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 B8P: 3-{3-[(pyridin-2-yl)methoxy]quinoxalin-2-yl}propanoic acid(Non-covalent)

B8P.4: 13 residues within 4Å: Chain A: E.35, W.37, G.48, R.49, Y.50, L.56, S.69, I.71, D.72, S.74, W.76, Y.78, Y.83 11 PLIP interactions: 11 interactions with chain A Hydrophobic interactions: A:W.37, A:R.49, A:I.71, A:W.76, A:Y.78 Hydrogen bonds: A:R.49, A:L.56 Water bridges: A:W.37, A:S.74, A:Y.83 pi-Stacking: A:W.37

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

UNX.5: 2 residues within 4Å: Chain A: G.28, D.29 Ligand excluded by PLIP UNX.6: 3 residues within 4Å: Chain A: G.28, Y.46 Ligands: UNX.7 Ligand excluded by PLIP UNX.7: 4 residues within 4Å: Chain A: Q.25, Q.44, V.45 Ligands: UNX.6 Ligand excluded by PLIP UNX.8: 1 residues within 4Å: Chain A: H.86 Ligand excluded by PLIP UNX.9: 3 residues within 4Å: Chain A: Y.46, H.58, N.61 Ligand excluded by PLIP UNX.10: 4 residues within 4Å: Chain A: S.2, P.3, Y.83 Ligands: UNX.16 Ligand excluded by PLIP UNX.11: 2 residues within 4Å: Chain A: V.11, A.12 Ligand excluded by PLIP UNX.12: 3 residues within 4Å: Chain A: H.9, Y.79 Ligands: UNX.19 Ligand excluded by PLIP UNX.13: 3 residues within 4Å: Chain A: P.3, S.74, Y.83 Ligand excluded by PLIP UNX.14: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP UNX.15: 3 residues within 4Å: Chain A: D.22, T.24, Q.25 Ligand excluded by PLIP UNX.16: 3 residues within 4Å: Chain A: A.82, Y.83 Ligands: UNX.10 Ligand excluded by PLIP UNX.17: 3 residues within 4Å: Chain A: C.30, G.31, T.32 Ligand excluded by PLIP UNX.18: 3 residues within 4Å: Chain A: C.30, N.52, H.54 Ligand excluded by PLIP UNX.19: 3 residues within 4Å: Chain A: P.8, H.9 Ligands: UNX.12 Ligand excluded by PLIP UNX.20: 1 residues within 4Å: Chain A: I.71 Ligand excluded by PLIP UNX.21: 2 residues within 4Å: Chain A: T.24, I.33 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Harding, R.J. et al., Small Molecule Antagonists of the Interaction between the Histone Deacetylase 6 Zinc-Finger Domain and Ubiquitin. J. Med. Chem. (2017)

Release Date

2017-08-23

Peptides

Histone deacetylase 6: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Histone deacetylase 6