Research workbench
Crystal structure of G303A HDAC8 in complex with M344
Analyse Crystal structure of G303A HDAC8 in complex with M344 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5THT
- Type
- protein
- Length
- 1,421 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Histone deacetylase 8
- EC
- 3.5.1.98
- UniProt
- Q9BY41
- Ligands
- B3N, K, ZN
- Pockets
- 10 · best druggability 0.81
Structure
x-ray diffraction · 4 distinct chains · 41% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Histone deacetylase 8 (EC 3.5.1.98) | protein | 361 | 42% helix, 13% strand | Q9BY41 |
| B | Histone deacetylase 8 (EC 3.5.1.98) | protein | 360 | 41% helix, 13% strand | Q9BY41 |
| C | Histone deacetylase 8 (EC 3.5.1.98) | protein | 353 | 40% helix, 13% strand | Q9BY41 |
| D | Histone deacetylase 8 (EC 3.5.1.98) | protein | 347 | 41% helix, 14% strand | Q9BY41 |
Ligands and binding sites
- B3N · 4-(dimethylamino)-N-[7-(hydroxyamino)-7-oxoheptyl]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
- EDO · 1,2-ethanediol · additive · 27 copies · chains A, B, D, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1033 | 0.81 | 0.82 | 97 | B3N, ZN, EDO |
| 2 | 482 | 0.69 | 0.79 | 63 | EDO |
| 3 | 84 | 0.66 | 0.91 | 19 | EDO |
| 4 | 67 | 0.63 | 0.92 | 19 | empty |
| 5 | 99 | 0.62 | 0.88 | 22 | EDO |
Interfaces
4 interfaces between chains.
- A–B · 809 Ų buried · 6 hydrogen bonds · protein-protein
- B–C · 403 Ų buried · 6 hydrogen bonds · protein-protein
- B–D · 365 Ų buried · 3 hydrogen bonds · protein-protein
- A–C · 97 Ų buried · 1 hydrogen bond · protein-protein
Compared structures
- 5THT · Crystal Structure of G303A HDAC8 in complex with M344 · 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 Q9BY41
- Elsewhere: RCSB PDB 5THT · PDBe 5THT · UniProt Q9BY41
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