MolNFT v1 · #184794 · protein
Tetartohedrally twinned crystal structure of schistosoma mansoni HDAC8 in complex with a tricyclic THIENO[3,2-B]INDOLE capped hydroxamate- based inhibitor, bromine derivative
7P2T · Histone deacetylase 8: “Tetartohedrally twinned crystal structure of schistosoma mansoni HDAC8 in complex with a tricyclic…”. X-ray diffraction, 4 ligands (4VX, K, ZN), 19 pockets (best druggability 0.81). MolNFT v1 #184794 on…
- PDB
- 7P2T
- Type
- protein
- Length
- 1,591 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Histone deacetylase 8
- UniProt
- A5H660
- Ligands
- 4VX, K, ZN, CL
- Pockets
- 19 · best druggability 0.81
Structure
x-ray diffraction · 4 distinct chains · 41% helix, 11% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Histone deacetylase 8 | protein | 402 | 42% helix, 11% strand | A5H660 |
| B | Histone deacetylase 8 | protein | 406 | 41% helix, 11% strand | A5H660 |
| C | Histone deacetylase 8 | protein | 409 | 38% helix, 11% strand | A5H660 |
| D | Histone deacetylase 8 | protein | 374 | 43% helix, 11% strand | A5H660 |
Ligands and binding sites
- 4VX · 5-[[(2R)-7-bromanyl-2-phenyl-2,3-dihydrothieno[3,2-b]indol-4-yl]methyl]-N-oxidanyl-thiophene-2-carboxamide · ligand · 4 copies · chains A, B, C, D
- K · Potassium ion · metal · 10 copies · chains A, B, C, D
- ZN · Zinc ion · metal · 4 copies · chains A, B, C, D
- CL · Chloride ion · ion · chains D
- 144 · Tris-hydroxymethyl-methyl-ammonium · additive · 2 copies · chains C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
19 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 941 | 0.81 | 0.82 | 101 | 4VX |
| 2 | 1040 | 0.80 | 0.82 | 108 | 4VX |
| 3 | 260 | 0.61 | 0.80 | 35 | empty |
| 4 | 338 | 0.59 | 0.77 | 46 | empty |
| 5 | 131 | 0.52 | 0.81 | 25 | empty |
Interfaces
4 interfaces between chains.
- A–B · 1192 Ų buried · 8 hydrogen bonds · protein-protein
- C–D · 1152 Ų buried · 10 hydrogen bonds · protein-protein
- B–C · 691 Ų buried · 8 hydrogen bonds · protein-protein
- A–D · 377 Ų buried · 2 hydrogen bonds · protein-protein
Compared structures
- 7P2T · Tetartohedrally twinned 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 7P2T · PDBe 7P2T · UniProt A5H660
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