Research workbench
Crystal structure of schistosoma mansoni HDAC8 in complex with a 3- chlorophenyl-spiroindoline capped hydroxamate-based inhibitor, bound to a novel site
Analyse Crystal structure of schistosoma mansoni HDAC8 in complex with a 3… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7P2U
- Type
- protein
- Length
- 409 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Histone deacetylase 8
- UniProt
- A5H660
- Ligands
- 4WB, K, ZN, CL
- Pockets
- 3 · best druggability 0.36
Structure
x-ray diffraction · 1 distinct chain · 42% helix, 12% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Histone deacetylase 8 | protein | 409 | 42% helix, 12% strand | A5H660 |
Ligands and binding sites
- 4WB · 5-[[(2R)-2-(3-chlorophenyl)-1'-methyl-spiro[2H-indole-3,4'-piperidine]-1-yl]methyl]-N-oxidanyl-thiophene-2-carboxamide · ligand · chains A
- K · Potassium ion · metal · 3 copies · chains A
- ZN · Zinc ion · metal · chains A
- CL · Chloride ion · ion · chains A
- TLA · L(+)-tartaric acid · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 58 | 0.36 | 0.79 | 19 | TLA |
| 2 | 51 | 0.31 | 0.77 | 16 | empty |
| 3 | 51 | 0.28 | 0.75 | 15 | empty |
Compared structures
- 7P2U · 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 7P2U · PDBe 7P2U · UniProt A5H660
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