SMTL ID : 6r0k.1

X-ray structure of Danio rerio histone deacetylase 6 (HDAC6) CD2 in complex with a inhibitor SS208

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.15 Å

Oligo State

monomer

Ligands

1 x ZN: ZINC ION(Non-covalent)

ZN.1: 4 residues within 4Å: Chain A: D.173, H.175, D.266 Ligands: JNN.4 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:D.173, A:D.173, A:H.175, A:D.266

2 x K: POTASSIUM ION(Non-covalent)

K.2: 6 residues within 4Å: Chain A: D.171, D.173, H.175, S.194, L.195, H.196 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:D.171, A:D.173, A:H.175, A:S.194, A:L.195 K.3: 4 residues within 4Å: Chain A: F.184, D.187, V.190, Y.223 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.187, A:V.190, A:Y.223, H2O.5, H2O.6

1 x JNN: 5-[2-[(3,4-dichlorophenyl)carbonylamino]ethyl]-~{N}-oxidanyl-1,2-oxazole-3-carboxamide(Non-covalent)

JNN.4: 14 residues within 4Å: Chain A: H.24, P.25, S.92, H.134, H.135, G.143, F.144, D.173, H.175, F.204, D.266, L.273, Y.306 Ligands: ZN.1 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:P.25, A:F.144, A:F.144, A:F.204, A:F.204 Hydrogen bonds: A:H.135 pi-Stacking: A:F.144

8 x SCN: THIOCYANATE ION(Non-functional Binders)

SCN.5: 7 residues within 4Å: Chain A: N.18, H.24, S.92, I.93, F.94, F.144 Ligands: SCN.7 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.18 SCN.6: 4 residues within 4Å: Chain A: W.20, P.80, R.81, N.84 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.84 SCN.7: 3 residues within 4Å: Chain A: D.88, I.93 Ligands: SCN.5 1 PLIP interactions: 1 interactions with chain A Water bridges: A:S.92 SCN.8: 2 residues within 4Å: Chain A: S.36, E.39 1 PLIP interactions: 1 interactions with chain A Water bridges: A:S.36 SCN.9: 7 residues within 4Å: Chain A: Q.181, E.185, K.214, V.215, G.216, L.217, N.224 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:G.216 Water bridges: A:Q.181 SCN.10: 1 residues within 4Å: Chain A: D.200 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:D.200 SCN.11: 2 residues within 4Å: Chain A: Q.289, S.292 No protein-ligand interaction detected (PLIP) SCN.12: 4 residues within 4Å: Chain A: R.12, A.52, R.53, L.54 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:R.12, A:R.12 Water bridges: A:D.10, A:L.54

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Shen, S. et al., Discovery of a New Isoxazole-3-hydroxamate-Based Histone Deacetylase 6 Inhibitor SS-208 with Antitumor Activity in Syngeneic Melanoma Mouse Models. J.Med.Chem. (2019)

Release Date

2019-10-09

Peptides

Histone deacetylase 6: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Histone deacetylase 6

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