SMTL ID : 5b8d.1

Crystal structure of a low occupancy fragment candidate (N-(4-Methyl-1,3-thiazol-2-yl)propanamide) bound adjacent to the ubiquitin binding pocket of the HDAC6 zinc-finger domain

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.05 Å

Oligo State

monomer

Ligands

3 x ZN: ZINC ION(Non-covalent)

ZN.1: 6 residues within 4Å: Chain A: C.39, C.42, H.58, H.64 Ligands: UNX.13, UNX.14 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:C.39, 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

2 x FMT: FORMIC ACID(Non-functional Binders)

FMT.4: 4 residues within 4Å: Chain A: W.37, G.48, R.49, Y.78 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.49, A:L.56 Water bridges: A:R.49 FMT.5: 4 residues within 4Å: Chain A: W.37, W.76, Y.83 Ligands: 6T4.6 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Y.83

1 x 6T4: ~{N}-(4-methyl-1,3-thiazol-2-yl)ethanamide(Non-covalent)

6T4.6: 8 residues within 4Å: Chain A: E.35, N.36, W.37, S.69, I.71, D.72, Y.83 Ligands: FMT.5 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:W.37, A:I.71 Hydrogen bonds: A:S.69, A:D.72

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

UNX.7: 3 residues within 4Å: Chain A: R.49, W.76 Ligands: UNX.30 Ligand excluded by PLIP UNX.8: 4 residues within 4Å: Chain A: P.17, A.18, A.19 Ligands: UNX.18 Ligand excluded by PLIP UNX.9: 6 residues within 4Å: Chain A: I.33, Q.34, E.35, N.36 Ligands: UNX.26, UNX.41 Ligand excluded by PLIP UNX.10: 4 residues within 4Å: Chain A: H.85 Ligands: UNX.20, UNX.35, UNX.36 Ligand excluded by PLIP UNX.11: 3 residues within 4Å: Chain A: I.16, A.18 Ligands: UNX.18 Ligand excluded by PLIP UNX.12: 2 residues within 4Å: Chain A: T.32, I.33 Ligand excluded by PLIP UNX.13: 8 residues within 4Å: Chain A: C.39, C.42, Y.43, Q.44, H.58, H.64 Ligands: ZN.1, UNX.14 Ligand excluded by PLIP UNX.14: 6 residues within 4Å: Chain A: C.42, Q.44, H.58, H.64 Ligands: ZN.1, UNX.13 Ligand excluded by PLIP UNX.15: 3 residues within 4Å: Chain A: I.71, K.100 Ligands: UNX.41 Ligand excluded by PLIP UNX.16: 2 residues within 4Å: Chain A: H.97 Ligands: UNX.17 Ligand excluded by PLIP UNX.17: 3 residues within 4Å: Chain A: L.73, H.97 Ligands: UNX.16 Ligand excluded by PLIP UNX.18: 4 residues within 4Å: Chain A: P.17, A.18 Ligands: UNX.8, UNX.11 Ligand excluded by PLIP UNX.19: 1 residues within 4Å: Chain A: H.9 Ligand excluded by PLIP UNX.20: 1 residues within 4Å: Ligands: UNX.10 Ligand excluded by PLIP UNX.21: 2 residues within 4Å: Chain A: P.26 Ligands: UNX.29 Ligand excluded by PLIP UNX.22: 4 residues within 4Å: Chain A: Q.34, E.35, I.71 Ligands: UNX.23 Ligand excluded by PLIP UNX.23: 2 residues within 4Å: Chain A: Q.34 Ligands: UNX.22 Ligand excluded by PLIP UNX.24: 5 residues within 4Å: Chain A: W.76, Y.78, Q.81 Ligands: UNX.27, UNX.30 Ligand excluded by PLIP UNX.25: 6 residues within 4Å: Chain A: T.32, I.33, Q.34, E.35, N.36, C.47 Ligand excluded by PLIP UNX.26: 5 residues within 4Å: Chain A: V.23, I.33, Y.70 Ligands: UNX.9, UNX.41 Ligand excluded by PLIP UNX.27: 3 residues within 4Å: Chain A: R.49 Ligands: UNX.24, UNX.30 Ligand excluded by PLIP UNX.28: 2 residues within 4Å: Chain A: Q.81, A.82 Ligand excluded by PLIP UNX.29: 2 residues within 4Å: Chain A: P.26 Ligands: UNX.21 Ligand excluded by PLIP UNX.30: 5 residues within 4Å: Chain A: R.49, Q.81 Ligands: UNX.7, UNX.24, UNX.27 Ligand excluded by PLIP UNX.31: 2 residues within 4Å: Chain A: W.6, V.11 Ligand excluded by PLIP UNX.32: 3 residues within 4Å: Chain A: H.9, C.80 Ligands: UNX.34 Ligand excluded by PLIP UNX.33: 3 residues within 4Å: Chain A: C.30, N.52, H.54 Ligand excluded by PLIP UNX.34: 1 residues within 4Å: Ligands: UNX.32 Ligand excluded by PLIP UNX.35: 5 residues within 4Å: Chain A: S.74, Y.83, H.85 Ligands: UNX.10, UNX.36 Ligand excluded by PLIP UNX.36: 3 residues within 4Å: Chain A: P.3 Ligands: UNX.10, UNX.35 Ligand excluded by PLIP UNX.37: 1 residues within 4Å: Ligands: NA.43 Ligand excluded by PLIP UNX.38: 2 residues within 4Å: Chain A: C.42, Y.43 Ligand excluded by PLIP UNX.39: 4 residues within 4Å: Chain A: Y.46, H.58, N.61 Ligands: UNX.40 Ligand excluded by PLIP UNX.40: 6 residues within 4Å: Chain A: D.29, Y.46, H.54, Q.57, H.58 Ligands: UNX.39 Ligand excluded by PLIP UNX.41: 6 residues within 4Å: Chain A: Y.70, I.71, K.100 Ligands: UNX.9, UNX.15, UNX.26 Ligand excluded by PLIP UNX.42: 3 residues within 4Å: Chain A: C.30, G.31, T.32 Ligand excluded by PLIP

1 x NA: SODIUM ION(Non-functional Binders)

NA.43: 3 residues within 4Å: Chain A: Y.50, I.51 Ligands: UNX.37 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:I.51

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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