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

Crystal Structure of Danio rerio Histone Deacetylase 6 Catalytic Domain 2 (CD2) Complexed with Bishydroxamic Acid Inhibitor

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.94 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: R5G.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: 6 residues within 4Å: Chain A: D.176, D.178, H.180, S.199, L.200, H.201 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:D.176, A:D.176, A:D.178, A:H.180, A:S.199 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.2

1 x R5G: N-hydroxy-1-{[4-(hydroxycarbamoyl)phenyl]methyl}-1H-indole-6-carboxamide(Non-covalent)

R5G.4: 14 residues within 4Å: Chain A: S.97, H.140, G.148, F.149, D.178, H.180, A.207, F.209, N.211, D.271, L.278, G.309, Y.311 Ligands: ZN.1 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:L.278 Hydrogen bonds: A:F.209, A:N.211, A:N.211, A:Y.311 pi-Stacking: A:F.149, A:H.180, A:F.209

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Morgen, M. et al., Design and Synthesis of Dihydroxamic Acids as HDAC6/8/10 Inhibitors. Chemmedchem (2020)

Release Date

2020-05-13

Peptides

Hdac6 protein: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

Hdac6 protein

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