SMTL ID : 6fyz.1 (2 other biounits)

Development and characterization of a CNS-penetrant benzhydryl hydroxamic acid class IIa histone deacetylase inhibitor

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.15 Å

Oligo State

monomer

Ligands

1 x EBE: (2~{S})-2-(2-fluorophenyl)-2-[4-(2-methylpyrimidin-5-yl)phenyl]-~{N}-oxidanyl-ethanamide(Non-covalent)

EBE.1: 17 residues within 4Å: Chain A: P.32, E.33, R.37, P.156, H.158, H.159, G.167, F.168, D.196, H.198, F.227, D.290, P.298, L.299, E.329, G.330 Ligands: ZN.2 11 PLIP interactions: 11 interactions with chain A Hydrophobic interactions: A:E.33, A:E.33, A:F.168, A:F.168, A:F.227, A:F.227, A:L.299 Hydrogen bonds: A:H.159 Water bridges: A:G.331 pi-Stacking: A:H.198, A:F.227

2 x ZN: ZINC ION(Non-covalent)

ZN.2: 4 residues within 4Å: Chain A: D.196, H.198, D.290 Ligands: EBE.1 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:D.196, A:D.196, A:H.198, A:D.290 ZN.3: 3 residues within 4Å: Chain A: C.23, C.25, H.31 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:C.23, A:C.25, A:H.31

1 x NA: SODIUM ION(Non-functional Binders)

NA.4: 4 residues within 4Å: Chain A: F.207, D.210, V.213, F.244 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:D.210, A:F.244

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Luckhurst, C.A. et al., Development and characterization of a CNS-penetrant benzhydryl hydroxamic acid class IIa histone deacetylase inhibitor. Bioorg. Med. Chem. Lett. (2019)

Release Date

2018-12-05

Peptides

Histone deacetylase 4: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Histone deacetylase 4

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