SMTL ID : 6dvm.3 (3 other biounits)

Crystal structure of Danio rerio histone deacetylase 6 catalytic domain 2 in complex with DDK-122

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.47 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: HBJ.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: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.192, A:V.195, A:Y.228, H2O.5, H2O.7

1 x HBJ: 4-(dimethylamino)-N-{[4-(hydroxycarbamoyl)phenyl]methyl}-N-{2-[(4-methylphenyl)amino]-2-oxoethyl}benzamide(Non-covalent)

HBJ.4: 14 residues within 4Å: Chain A: D.26, P.30, S.97, H.140, G.148, F.149, D.178, H.180, F.209, D.271, L.278, G.309, Y.311 Ligands: ZN.1 9 PLIP interactions: 9 interactions with chain A Hydrophobic interactions: A:P.30, A:F.209, A:L.278, A:L.278 Hydrogen bonds: A:H.180, A:Y.311 Water bridges: A:S.97, A:F.209 pi-Stacking: A:F.149

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

EDO.5: 3 residues within 4Å: Chain A: N.89, R.90, D.93 3 PLIP interactions: 3 interactions with chain A Water bridges: A:R.86, A:R.86, A:D.93 EDO.6: 5 residues within 4Å: Chain A: L.123, R.167, L.170, E.262, R.302 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:L.123, A:R.167, A:E.262 EDO.7: 4 residues within 4Å: Chain A: I.76, L.91, E.94, Y.95 1 PLIP interactions: 1 interactions with chain A Water bridges: A:E.94 EDO.8: 5 residues within 4Å: Chain A: A.66, L.67, C.68, H.69, K.143 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:H.69 EDO.9: 1 residues within 4Å: Chain A: R.354 No protein-ligand interaction detected (PLIP)

1 x BTB: 2-[BIS-(2-HYDROXY-ETHYL)-AMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL(Non-covalent)

BTB.10: 2 residues within 4Å: Chain A: Q.16, R.17 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:Q.16, A:Q.16, A:R.17, A:R.17

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Porter, N.J. et al., Histone Deacetylase 6-Selective Inhibitors and the Influence of Capping Groups on Hydroxamate-Zinc Denticity. J. Med. Chem. (2018)

Release Date

2018-08-29

Peptides

Hdac6 protein: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
C

Hdac6 protein

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