SMTL ID : 5kh3.1

Crystal structure of fragment (3-(5-Chloro-1,3-benzothiazol-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

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

UNX.4: 4 residues within 4Å: Chain A: I.33, Q.34, E.35, N.36 No protein-ligand interaction detected (PLIP) UNX.5: 2 residues within 4Å: Chain A: H.86, Q.87 No protein-ligand interaction detected (PLIP) UNX.6: 1 residues within 4Å: Chain A: A.19 No protein-ligand interaction detected (PLIP) UNX.7: 5 residues within 4Å: Chain A: S.74, A.75, V.84, K.93 Ligands: UNX.16 No protein-ligand interaction detected (PLIP) UNX.8: 2 residues within 4Å: Chain A: L.73, H.97 No protein-ligand interaction detected (PLIP) UNX.9: 3 residues within 4Å: Chain A: Y.50, I.51 Ligands: UNX.10 No protein-ligand interaction detected (PLIP) UNX.10: 4 residues within 4Å: Chain A: Y.50, I.51 Ligands: UNX.9, UNX.12 No protein-ligand interaction detected (PLIP) UNX.11: 2 residues within 4Å: Chain A: C.42, Y.43 No protein-ligand interaction detected (PLIP) UNX.12: 3 residues within 4Å: Chain A: I.51, N.52 Ligands: UNX.10 No protein-ligand interaction detected (PLIP) UNX.13: 2 residues within 4Å: Chain A: W.6, L.10 No protein-ligand interaction detected (PLIP) UNX.14: 2 residues within 4Å: Chain A: W.6, H.86 No protein-ligand interaction detected (PLIP) UNX.15: 4 residues within 4Å: Chain A: D.29, Y.46, Q.57, N.61 No protein-ligand interaction detected (PLIP) UNX.16: 3 residues within 4Å: Chain A: S.74, Y.83 Ligands: UNX.7 No protein-ligand interaction detected (PLIP)

1 x 6U6: 3-(5-chloranyl-1,3-benzothiazol-2-yl)propanoic acid(Non-covalent)

6U6.17: 8 residues within 4Å: Chain A: E.35, W.37, G.48, R.49, L.56, W.76, Y.78, Y.83 12 PLIP interactions: 12 interactions with chain A Hydrophobic interactions: A:W.37, A:W.76, A:Y.78 Hydrogen bonds: A:E.35, A:R.49, A:L.56 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

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

2016-07-27

Peptides

Histone deacetylase 6: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Histone deacetylase 6

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