SMTL ID : 6cgp.1

Crystal structure of Danio rerio histone deacetylase 6 catalytic domain 2 complexed with MAIP-032

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.50 Å

Oligo State

monomer

Ligands

2 x K: POTASSIUM ION(Non-covalent)

K.1: 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.176, A:H.180, A:S.199, A:L.200 K.2: 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.1, H2O.1

1 x ZN: ZINC ION(Non-covalent)

ZN.3: 4 residues within 4Å: Chain A: D.178, H.180, D.271 Ligands: F1Y.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

1 x F1Y: N-hydroxy-4-[(2-propylimidazo[1,2-a]pyridin-3-yl)amino]benzamide(Non-covalent)

F1Y.4: 14 residues within 4Å: Chain A: 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.3, EDO.5 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:P.30, A:F.209 Hydrogen bonds: A:S.97, A:S.97 pi-Stacking: A:F.149

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

EDO.5: 3 residues within 4Å: Chain A: N.96, S.97 Ligands: F1Y.4 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.96, A:S.97

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Mackwitz, M.K.W. et al., Multicomponent Synthesis and Binding Mode of Imidazo[1,2- a]pyridine-Capped Selective HDAC6 Inhibitors. Org. Lett. (2018)

Release Date

2018-06-13

Peptides

Hdac6 protein: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Hdac6 protein

Related Entries With Identical Sequence