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
- 4CBY
- Type
- protein
- Length
- 1,523 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Histone deacetylase 4
- EC
- 3.5.1.98
- UniProt
- P56524
- Ligands
- KEE, ZN, NA
- Pockets
- 10 · best druggability 0.78
Structure
x-ray diffraction · 3 distinct chains · 42% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Histone deacetylase 4 (EC 3.5.1.98) | protein | 380 | 43% helix, 13% strand | P56524 |
| B | Histone deacetylase 4 (EC 3.5.1.98) | protein | 380 | 42% helix, 13% strand | P56524 |
| D | Histone deacetylase 4 (EC 3.5.1.98) | protein | 383 | 42% helix, 13% strand | P56524 |
Ligands and binding sites
- KEE · (1R,2R,3R)-2-[4-(1,3-oxazol-5-yl)phenyl]-N-oxidanyl-3-phenyl-cyclopropane-1-carboxamide · ligand · 4 copies · chains A, B, C, D
- ZN · Zinc ion · metal · 8 copies · chains A, B, C, D
- NA · Sodium ion · metal · 8 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 804 | 0.78 | 0.81 | 82 | empty |
| 2 | 347 | 0.70 | 0.83 | 58 | KEE |
| 3 | 566 | 0.68 | 0.78 | 49 | empty |
| 4 | 385 | 0.65 | 0.79 | 40 | empty |
| 5 | 132 | 0.64 | 0.87 | 20 | KEE, ZN |
Interfaces
5 interfaces between chains.
- A–D · 695 Ų buried · 2 hydrogen bonds · protein-protein
- B–C · 541 Ų buried · 10 hydrogen bonds · protein-protein
- B–D · 360 Ų buried · 4 hydrogen bonds · protein-protein
- A–C · 329 Ų buried · 6 hydrogen bonds · protein-protein
- C–D · 38 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 4CBY · 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 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 4CBY · PDBe 4CBY · UniProt P56524
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