MolNFT v1 · #151571 · protein
Crystal structure of schistosoma mansoni HDAC8 complexed with ncc-149
6HRQ · Histone deacetylase: “Crystal structure of schistosoma mansoni HDAC8 complexed with ncc-149”. X-ray diffraction, 3 ligands (GM5, K, ZN), 15 pockets (best druggability 0.80). MolNFT v1 #151571 on GenesisL1: 3D structure, binding…
- PDB
- 6HRQ
- Type
- protein
- Length
- 1,636 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
- GM5, K, ZN
- Pockets
- 15 · best druggability 0.80
Structure
x-ray diffraction · 4 distinct chains · 42% helix, 12% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Histone deacetylase (EC 3.5.1.98) | protein | 401 | 42% helix, 12% strand | A5H660 |
| B | Histone deacetylase (EC 3.5.1.98) | protein | 416 | 43% helix, 13% strand | A5H660 |
| C | Histone deacetylase (EC 3.5.1.98) | protein | 419 | 41% helix, 12% strand | A5H660 |
| D | Histone deacetylase (EC 3.5.1.98) | protein | 400 | 42% helix, 13% strand | A5H660 |
Ligands and binding sites
- GM5 · ~{N}-oxidanyl-3-[1-(phenylsulfanylmethyl)-1,2,3-triazol-4-yl]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 · 28 copies · chains A, B, C, D
- 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
15 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1151 | 0.80 | 0.82 | 106 | ZN, GM5, DMF, GOL |
| 2 | 1130 | 0.80 | 0.81 | 110 | ZN, GM5, DMF, GOL |
| 3 | 288 | 0.60 | 0.79 | 39 | empty |
| 4 | 235 | 0.57 | 0.78 | 33 | DMF |
| 5 | 182 | 0.44 | 0.74 | 23 | empty |
Interfaces
4 interfaces between chains.
- C–D · 1069 Ų buried · 9 hydrogen bonds · protein-protein
- A–B · 1025 Ų buried · 8 hydrogen bonds · protein-protein
- A–C · 356 Ų buried · 1 hydrogen bond · protein-protein
- B–D · 346 Ų buried · 2 hydrogen bonds · protein-protein
Compared structures
- 6HRQ · Crystal structure of Schistosoma mansoni HDAC8 complexed with NCC-149 · 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 6HRQ · PDBe 6HRQ · UniProt A5H660
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