Research workbench
Potent, selective and cns-penetrant tetrasubstituted cyclopropane class iia histone deacetylase (hdac) inhibitors
Analyse Potent, selective and cns-penetrant tetrasubstituted cyclopropane class iia… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5A2S
- Type
- protein
- Length
- 760 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Histone deacetylase 4
- EC
- 3.5.1.98
- UniProt
- P56524
- Ligands
- OTF, ZN, NA
- Pockets
- 3 · best druggability 0.78
Structure
x-ray diffraction · 1 distinct chain · 42% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Histone deacetylase 4 (EC 3.5.1.98) | protein | 380 | 42% helix, 13% strand | P56524 |
Ligands and binding sites
- OTF · (1S,2S,3S)-1-fluoranyl-2-[4-(5-fluoranylpyrimidin-2-yl)phenyl]-N-oxidanyl-3-phenyl-cyclopropane-1-carboxamide · ligand · 2 copies · chains A, B
- ZN · Zinc ion · metal · 4 copies · chains A, B
- NA · Sodium ion · metal · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 839 | 0.78 | 0.81 | 73 | empty |
| 2 | 144 | 0.64 | 0.86 | 22 | OTF |
| 3 | 126 | 0.62 | 0.86 | 22 | OTF, ZN |
Interfaces
1 interface between chains.
- A–B · 653 Ų buried · 9 hydrogen bonds · protein-protein
Compared structures
- 5A2S · Potent, selective and CNS-penetrant tetrasubstituted cyclopropane class IIa histone… · the same entry in another collection · chain A against A, TM-score 1.00
- P56524 · AlphaFold monomer V2.0 prediction for histone deacetylase 4 (P56524) · a predicted model of the same protein · chain A against A, TM-score 0.98
Analyse
- Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
- Every structure of UniProt P56524
- Elsewhere: RCSB PDB 5A2S · PDBe 5A2S · UniProt P56524
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