SMTL ID : 6cw8.2 (1 other biounit)

Crystal structure of Danio rerio histone deacetylase 6 catalytic domain 2 complexed with RTS-V5

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.90 Å

Oligo State

monomer

Ligands

1 x ZN: ZINC ION(Non-covalent)

ZN.1: 4 residues within 4Å: Chain A: D.178, H.180, D.271 Ligands: FGY.4 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.178, A:D.178, A:H.180, A:D.271, H2O.1

2 x K: POTASSIUM ION(Non-covalent)

K.2: 5 residues within 4Å: Chain A: D.176, D.178, H.180, S.199, L.200 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:D.176, A:D.178, A:H.180, A:S.199, A:L.200 K.3: 4 residues within 4Å: Chain A: F.189, D.192, V.195, Y.228 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:F.189, A:D.192, A:V.195, A:Y.228, H2O.4

1 x FGY: N-(2,2-dimethylpropyl)-N~2~-[4-(hydroxycarbamoyl)benzene-1-carbonyl]-L-asparaginyl-N-benzyl-L-alaninamide(Non-covalent)

FGY.4: 18 residues within 4Å: Chain A: H.29, P.30, N.96, S.97, H.140, G.148, F.149, D.178, H.180, F.209, N.211, D.271, L.278, G.309, Y.311 Ligands: ZN.1, EDO.7, EDO.8 13 PLIP interactions: 13 interactions with chain A Hydrophobic interactions: A:P.30, A:N.96, A:F.149, A:F.209, A:F.209, A:L.278 Hydrogen bonds: A:N.96, A:S.97, A:S.97, A:Y.311 Water bridges: A:N.96, A:S.97 pi-Stacking: A:F.149

4 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.5: 5 residues within 4Å: Chain A: M.19, L.20, H.22, P.33, E.103 No protein-ligand interaction detected (PLIP) EDO.6: 7 residues within 4Å: Chain A: W.25, N.89, G.92, D.93, I.98, F.99 Ligands: EDO.7 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.89 Water bridges: A:G.92, A:G.92 EDO.7: 8 residues within 4Å: Chain A: H.29, S.97, I.98, F.99, F.149 Ligands: FGY.4, EDO.6, EDO.8 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:H.29 EDO.8: 3 residues within 4Å: Chain A: N.96 Ligands: FGY.4, EDO.7 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.96 Water bridges: A:D.93

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Bhatia, S. et al., Discovery of the First-in-Class Dual Histone Deacetylase-Proteasome Inhibitor. J. Med. Chem. (2018)

Release Date

2018-11-21

Peptides

Hdac6 protein: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

Hdac6 protein

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