MolNFT v1 · #149384 · protein
Development and characterization of a cns-penetrant benzhydryl hydroxamic acid class iia histone deacetylase inhibitor
6FYZ · Histone deacetylase 4: “Development and characterization of a cns-penetrant benzhydryl hydroxamic acid class iia histone deacetylase…”. X-ray diffraction, 3 ligands (EBE, ZN, NA), 9 pockets (best druggability 0.72). MolNFT v1…
- PDB
- 6FYZ
- Type
- protein
- Length
- 1,058 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
- EBE, ZN, NA
- Pockets
- 9 · best druggability 0.72
Structure
x-ray diffraction · 3 distinct chains · 41% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Histone deacetylase 4 (EC 3.5.1.98) | protein | 345 | 41% helix, 14% strand | P56524 |
| B | Histone deacetylase 4 (EC 3.5.1.98) | protein | 364 | 40% helix, 14% strand | P56524 |
| C | Histone deacetylase 4 (EC 3.5.1.98) | protein | 349 | 42% helix, 14% strand | P56524 |
Ligands and binding sites
- EBE · (2~{S})-2-(2-fluorophenyl)-2-[4-(2-methylpyrimidin-5-yl)phenyl]-~{N}-oxidanyl-ethanamide · ligand · 3 copies · chains A, B, C
- ZN · Zinc ion · metal · 6 copies · chains A, B, C
- NA · Sodium ion · metal · 3 copies · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1049 | 0.72 | 0.75 | 69 | empty |
| 2 | 105 | 0.64 | 0.89 | 20 | EBE |
| 3 | 108 | 0.63 | 0.88 | 20 | EBE |
| 4 | 133 | 0.62 | 0.85 | 21 | EBE |
| 5 | 236 | 0.49 | 0.74 | 32 | empty |
Interfaces
3 interfaces between chains.
- A–B · 687 Ų buried · 8 hydrogen bonds · protein-protein
- B–C · 390 Ų buried · 5 hydrogen bonds · protein-protein
- A–C · 60 Ų buried · 1 hydrogen bond · protein-protein
Compared structures
- 6FYZ · Development and characterization of a CNS-penetrant benzhydryl hydroxamic acid class IIa… · 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 0.99
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 6FYZ · PDBe 6FYZ · UniProt P56524
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