MolNFT v1 · #106035 · protein
Crystal structure of S39D HDAC8 in complex with a largazole analogue.
4RN2 · Histone deacetylase 8: “Crystal structure of S39D HDAC8 in complex with a largazole analogue.”. X-ray diffraction, 3 ligands (L7G, K, ZN), 4 pockets (best druggability 0.75). MolNFT v1 #106035 on GenesisL1: 3D structure, binding…
- PDB
- 4RN2
- Type
- protein
- Length
- 706 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Histone deacetylase 8
- EC
- 3.5.1.98
- UniProt
- Q9BY41
- Ligands
- L7G, K, ZN
- Pockets
- 4 · best druggability 0.75
Structure
x-ray diffraction · 2 distinct chains · 41% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Histone deacetylase 8 (EC 3.5.1.98) | protein | 349 | 40% helix, 13% strand | Q9BY41 |
| B | Histone deacetylase 8 (EC 3.5.1.98) | protein | 357 | 41% helix, 13% strand | Q9BY41 |
Ligands and binding sites
- L7G · (5R,8S,11S)-5-methyl-8-(propan-2-yl)-11-[(1E)-4-sulfanylbut-1-en-1-yl]-3-thia-7,10,14,17,21-pentaazatricyclo[14.3.1.1~2,5~]henicosa-1(20),2(21),16,18-tetraene-6,9,13-trione · ligand · 2 copies · chains A, B
- K · Potassium ion · metal · 4 copies · chains A, B
- ZN · Zinc ion · metal · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 66 | 0.75 | 0.99 | 25 | empty |
| 2 | 1060 | 0.73 | 0.76 | 85 | L7G |
| 3 | 115 | 0.59 | 0.85 | 30 | empty |
| 4 | 56 | 0.27 | 0.73 | 12 | empty |
Interfaces
1 interface between chains.
- A–B · 653 Ų buried · 2 hydrogen bonds · protein-protein
Compared structures
- 4RN2 · Crystal structure of S39D HDAC8 in complex with a largazole analogue. · 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 4RN2 · PDBe 4RN2 · UniProt Q9BY41
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