Research workbench
Design, synthesis, and biological evaluation of potent and selective class iia hdac inhibitors as a potential therapy for HUNTINGTON'S disease
Analyse Design, synthesis, and biological evaluation of potent and selective class iia… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4CBT
- Type
- protein
- Length
- 1,047 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Histone deacetylase 4
- EC
- 3.5.1.98
- UniProt
- P56524
- Ligands
- 9F4, ZN
- Pockets
- 8 · best druggability 0.71
Structure
x-ray diffraction · 3 distinct chains · 41% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Histone deacetylase 4 (EC 3.5.1.98) | protein | 349 | 41% helix, 13% strand | P56524 |
| B | Histone deacetylase 4 (EC 3.5.1.98) | protein | 352 | 41% helix, 13% strand | P56524 |
| C | Histone deacetylase 4 (EC 3.5.1.98) | protein | 346 | 40% helix, 13% strand | P56524 |
Ligands and binding sites
- 9F4 · (1R,2R,3R)-2-[4-(5-fluoranylpyrimidin-2-yl)phenyl]-N-oxidanyl-3-phenyl-cyclopropane-1-carboxamide · ligand · 3 copies · chains A, B, C
- ZN · Zinc ion · metal · 6 copies · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1152 | 0.71 | 0.75 | 67 | empty |
| 2 | 113 | 0.66 | 0.89 | 20 | 9F4 |
| 3 | 127 | 0.64 | 0.87 | 20 | 9F4 |
| 4 | 116 | 0.62 | 0.87 | 20 | 9F4 |
| 5 | 229 | 0.49 | 0.75 | 40 | empty |
Interfaces
3 interfaces between chains.
- A–B · 702 Ų buried · 8 hydrogen bonds · protein-protein
- B–C · 414 Ų buried · 4 hydrogen bonds · protein-protein
- A–C · 69 Ų buried · 1 hydrogen bond · protein-protein
Compared structures
- 4CBT · Design, synthesis, and biological evaluation of potent and selective Class IIa HDAC… · 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 B against A, TM-score 0.99
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 4CBT · PDBe 4CBT · UniProt P56524
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