MolNFT v1 · #184796 · protein
Crystal structure of schistosoma mansoni HDAC8 in complex with a 4- chlorophenyl-spiroindoline capped hydroxamate-based inhibitor, bound to a novel site
7P2V · Histone deacetylase 8: “Crystal structure of schistosoma mansoni HDAC8 in complex with a 4- chlorophenyl-spiroindoline capped…”. X-ray diffraction, 3 ligands (4XI, K, ZN), 1 pocket (best druggability 0.28). MolNFT v1 #184796 on…
- PDB
- 7P2V
- Type
- protein
- Length
- 385 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Histone deacetylase 8
- UniProt
- A5H660
- Ligands
- 4XI, K, ZN
- Pockets
- 1 · best druggability 0.28
Structure
x-ray diffraction · 1 distinct chain · 43% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Histone deacetylase 8 | protein | 385 | 43% helix, 13% strand | A5H660 |
Ligands and binding sites
- 4XI · 5-[[(2S)-2-(4-chlorophenyl)-1'-methyl-spiro[2H-indole-3,4'-piperidine]-1-yl]methyl]-N-oxidanyl-thiophene-2-carboxamide · ligand · chains A
- K · Potassium ion · metal · 2 copies · chains A
- ZN · Zinc ion · metal · chains A
- TLA · L(+)-tartaric acid · additive · chains A
- PEG · Di(hydroxyethyl)ether · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
1 pocket found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 55 | 0.28 | 0.74 | 15 | empty |
Compared structures
- 7P2V · Crystal structure of Schistosoma mansoni HDAC8 in complex with a… · 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 7P2V · PDBe 7P2V · UniProt A5H660
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