SMTL ID : 6q0z.2 (1 other biounit)

Crystal structure of Danio rerio histone deacetylase 6 catalytic domain 2 complexed with JS28

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.75 Å

Oligo State

monomer

Ligands

1 x ZN: ZINC ION(Non-covalent)

ZN.1: 4 residues within 4Å: Chain A: D.171, H.173, D.264 Ligands: P7V.4 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:D.171, A:D.171, A:H.173, A:D.264

2 x K: POTASSIUM ION(Non-covalent)

K.2: 6 residues within 4Å: Chain A: D.169, D.171, H.173, S.192, L.193, H.194 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:D.169, A:D.171, A:H.173, A:S.192, A:L.193 K.3: 4 residues within 4Å: Chain A: F.182, D.185, V.188, Y.221 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.185, A:V.188, A:Y.221, H2O.4, H2O.5

1 x P7V: 2-(4-bromophenyl)-N-hydroxy-1,3-oxazole-4-carboxamide(Non-covalent)

P7V.4: 12 residues within 4Å: Chain A: S.90, H.132, H.133, G.141, F.142, D.171, H.173, F.202, D.264, L.271, Y.304 Ligands: ZN.1 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:F.142, A:L.271 Hydrogen bonds: A:H.133, A:Y.304 pi-Stacking: A:F.142, A:H.173, A:F.202

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Osko, J.D. et al., Exploring Structural Determinants of Inhibitor Affinity and Selectivity in Complexes with Histone Deacetylase 6. J.Med.Chem. (2020)

Release Date

2020-02-05

Peptides

Hdac6 protein: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

Hdac6 protein

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