SMTL ID : 5kh9.1

Crystal structure of a low occupancy fragment candidate (5-[(4-Isopropylphenyl)amino]-6-methyl-1,2,4-triazin-3(2H)-one) bound in the ubiquitin binding pocket of the HDAC6 zinc-finger domain

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.07 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.6, UNX.7 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

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

FMT.4: 4 residues within 4Å: Chain A: W.37, G.48, R.49, Y.78 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:R.49, A:R.49, A:Y.78 Water bridges: A:L.56

1 x 6T5: 6-methyl-5-[(4-propan-2-ylphenyl)amino]-2~{H}-1,2,4-triazin-3-one(Non-covalent)

6T5.5: 5 residues within 4Å: Chain A: W.37, R.49, W.76, Y.83 Ligands: UNX.33 9 PLIP interactions: 9 interactions with chain A Hydrophobic interactions: A:W.37, A:W.76, A:Y.83, A:Y.83 Hydrogen bonds: A:Y.83, A:Y.83 Water bridges: A:W.76 pi-Stacking: A:W.76 pi-Cation interactions: A:R.49

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

UNX.6: 8 residues within 4Å: Chain A: C.39, C.42, Y.43, Q.44, H.58, H.64 Ligands: ZN.1, UNX.7 Ligand excluded by PLIP UNX.7: 7 residues within 4Å: Chain A: C.42, Q.44, H.58, H.64 Ligands: ZN.1, UNX.6, UNX.37 Ligand excluded by PLIP UNX.8: 3 residues within 4Å: Chain A: P.17, A.18 Ligands: UNX.27 Ligand excluded by PLIP UNX.9: 2 residues within 4Å: Chain A: D.72, L.73 Ligand excluded by PLIP UNX.10: 2 residues within 4Å: Chain A: H.9 Ligands: UNX.15 Ligand excluded by PLIP UNX.11: 2 residues within 4Å: Chain A: P.8 Ligands: UNX.31 Ligand excluded by PLIP UNX.12: 2 residues within 4Å: Chain A: T.32 Ligands: UNX.32 Ligand excluded by PLIP UNX.13: 5 residues within 4Å: Chain A: Y.46, H.58, N.61 Ligands: UNX.16, UNX.20 Ligand excluded by PLIP UNX.14: 1 residues within 4Å: Chain A: A.19 Ligand excluded by PLIP UNX.15: 3 residues within 4Å: Chain A: Y.79 Ligands: UNX.10, UNX.30 Ligand excluded by PLIP UNX.16: 5 residues within 4Å: Chain A: D.29, H.54, Q.57, H.58 Ligands: UNX.13 Ligand excluded by PLIP UNX.17: 2 residues within 4Å: Chain A: H.97, F.101 Ligand excluded by PLIP UNX.18: 4 residues within 4Å: Chain A: I.51, N.52 Ligands: UNX.19, NA.39 Ligand excluded by PLIP UNX.19: 4 residues within 4Å: Chain A: Y.50, I.51 Ligands: UNX.18, NA.39 Ligand excluded by PLIP UNX.20: 3 residues within 4Å: Chain A: H.58, N.61 Ligands: UNX.13 Ligand excluded by PLIP UNX.21: 1 residues within 4Å: Chain A: Q.34 Ligand excluded by PLIP UNX.22: 1 residues within 4Å: Chain A: H.64 Ligand excluded by PLIP UNX.23: 2 residues within 4Å: Chain A: H.59, G.60 Ligand excluded by PLIP UNX.24: 1 residues within 4Å: Chain A: N.61 Ligand excluded by PLIP UNX.25: 1 residues within 4Å: Chain A: E.35 Ligand excluded by PLIP UNX.26: 5 residues within 4Å: Chain A: C.39, H.58, H.59, H.64, V.67 Ligand excluded by PLIP UNX.27: 4 residues within 4Å: Chain A: P.17, A.18, A.19 Ligands: UNX.8 Ligand excluded by PLIP UNX.28: 3 residues within 4Å: Chain A: D.22, T.24, Q.25 Ligand excluded by PLIP UNX.29: 3 residues within 4Å: Chain A: P.15, I.16 Ligands: UNX.34 Ligand excluded by PLIP UNX.30: 3 residues within 4Å: Chain A: Y.79 Ligands: UNX.15, UNX.31 Ligand excluded by PLIP UNX.31: 4 residues within 4Å: Chain A: H.9, C.80 Ligands: UNX.11, UNX.30 Ligand excluded by PLIP UNX.32: 3 residues within 4Å: Chain A: T.32, I.33 Ligands: UNX.12 Ligand excluded by PLIP UNX.33: 2 residues within 4Å: Chain A: Q.81 Ligands: 6T5.5 Ligand excluded by PLIP UNX.34: 5 residues within 4Å: Chain A: V.13, C.14, I.16, Y.43 Ligands: UNX.29 Ligand excluded by PLIP UNX.35: 1 residues within 4Å: Chain A: L.4 Ligand excluded by PLIP UNX.36: 2 residues within 4Å: Chain A: D.91, N.94 Ligand excluded by PLIP UNX.37: 2 residues within 4Å: Chain A: C.42 Ligands: UNX.7 Ligand excluded by PLIP UNX.38: 1 residues within 4Å: Ligands: NA.39 Ligand excluded by PLIP

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

NA.39: 5 residues within 4Å: Chain A: Y.50, I.51 Ligands: UNX.18, UNX.19, UNX.38 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Y.50

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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