MolNFT v1 · #88296 · protein
Crystal structure of schistosoma mansoni HDAC8 complexed with a mercaptoacetamide inhibitor
4CQF · Histone deacetylase 8: “Crystal structure of schistosoma mansoni HDAC8 complexed with a mercaptoacetamide inhibitor”. X-ray diffraction, 3 ligands (9Z8, K, ZN), 14 pockets (best druggability 0.78). MolNFT v1 #88296 on GenesisL1: 3D…
- PDB
- 4CQF
- Type
- protein
- Length
- 1,628 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Histone deacetylase 8
- UniProt
- A5H660
- Ligands
- 9Z8, K, ZN
- Pockets
- 14 · best druggability 0.78
Structure
x-ray diffraction · 4 distinct chains · 43% helix, 12% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Histone deacetylase 8 | protein | 398 | 43% helix, 13% strand | A5H660 |
| B | Histone deacetylase 8 | protein | 413 | 43% helix, 12% strand | A5H660 |
| C | Histone deacetylase 8 | protein | 417 | 42% helix, 12% strand | A5H660 |
| D | Histone deacetylase 8 | protein | 400 | 43% helix, 13% strand | A5H660 |
Ligands and binding sites
- 9Z8 · 6-(2-Mercaptoacetylamino)-N-phenylhexanamide · 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 · 11 copies · chains A, B, C, D
- GOL · Glycerol · additive · 7 copies · chains B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
14 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1127 | 0.78 | 0.80 | 111 | 9Z8, GOL |
| 2 | 1198 | 0.78 | 0.79 | 116 | 9Z8, GOL |
| 3 | 388 | 0.64 | 0.79 | 38 | GOL |
| 4 | 310 | 0.62 | 0.79 | 36 | empty |
| 5 | 89 | 0.44 | 0.80 | 17 | empty |
Interfaces
4 interfaces between chains.
- C–D · 1077 Ų buried · 7 hydrogen bonds · protein-protein
- A–B · 1015 Ų buried · 8 hydrogen bonds · protein-protein
- B–D · 452 Ų buried · 3 hydrogen bonds · protein-protein
- A–C · 446 Ų buried · 4 hydrogen bonds · protein-protein
Compared structures
- 4CQF · Crystal structure of Schistosoma mansoni HDAC8 complexed with a mercaptoacetamide… · 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 4CQF · PDBe 4CQF · UniProt A5H660
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