MolNFT v1 · #151627 · protein
Crystal structure of schistosoma mansoni HDAC8 complexed with a benzohydroxamate inhibitor 5
6HTH · Histone deacetylase: “Crystal structure of schistosoma mansoni HDAC8 complexed with a benzohydroxamate inhibitor 5”. X-ray diffraction, 3 ligands (GQN, K, ZN), 11 pockets (best druggability 0.80). MolNFT v1 #151627 on GenesisL1: 3D…
- PDB
- 6HTH
- Type
- protein
- Length
- 1,587 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Histone deacetylase
- EC
- 3.5.1.98
- UniProt
- A5H660
- Ligands
- GQN, K, ZN
- Pockets
- 11 · best druggability 0.80
Structure
x-ray diffraction · 4 distinct chains · 43% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Histone deacetylase (EC 3.5.1.98) | protein | 386 | 44% helix, 13% strand | A5H660 |
| B | Histone deacetylase (EC 3.5.1.98) | protein | 410 | 42% helix, 12% strand | A5H660 |
| C | Histone deacetylase (EC 3.5.1.98) | protein | 407 | 43% helix, 12% strand | A5H660 |
| D | Histone deacetylase (EC 3.5.1.98) | protein | 384 | 43% helix, 13% strand | A5H660 |
Ligands and binding sites
- GQN · 4-methoxy-~{N}-oxidanyl-3-[(4-phenylphenyl) carbonylamino]benzamide · ligand · 4 copies · chains A, B, C, D
- K · Potassium ion · metal · 8 copies · chains A, B, C, D
- ZN · Zinc ion · metal · 4 copies · chains A, B, C, D
- DMF · Dimethylformamide · additive · 19 copies · chains A, B, D, C
- GOL · Glycerol · additive · 13 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 981 | 0.80 | 0.81 | 101 | GQN, GOL, DMF |
| 2 | 1111 | 0.79 | 0.81 | 120 | ZN, GQN, DMF |
| 3 | 339 | 0.58 | 0.76 | 46 | DMF |
| 4 | 329 | 0.56 | 0.75 | 43 | empty |
| 5 | 197 | 0.45 | 0.73 | 24 | empty |
Interfaces
4 interfaces between chains.
- C–D · 1008 Ų buried · 10 hydrogen bonds · protein-protein
- A–B · 911 Ų buried · 13 hydrogen bonds · protein-protein
- B–D · 341 Ų buried · 3 hydrogen bonds · protein-protein
- A–C · 331 Ų buried · 2 hydrogen bonds · protein-protein
Compared structures
- 6HTH · Crystal structure of Schistosoma mansoni HDAC8 complexed with a benzohydroxamate… · the same entry in another collection · chain A against A, TM-score 1.00
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 A5H660
- Elsewhere: RCSB PDB 6HTH · PDBe 6HTH · UniProt A5H660
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.