Research workbench
Structure of human HDAC2 in complex with ketone inhibitor (compound O)
Analyse Structure of human HDAC2 in complex with ketone inhibitor (compound O) in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6XEC
- Type
- protein
- Length
- 1,100 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Histone deacetylase 2
- EC
- 3.5.1.98
- UniProt
- Q92769
- Ligands
- V1S, CA, ZN, SO4
- Pockets
- 6 · best druggability 0.72
Structure
x-ray diffraction · 2 distinct chains · 40% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Histone deacetylase 2 (EC 3.5.1.98) | protein | 368 | 39% helix, 13% strand | Q92769 |
| B, C | Histone deacetylase 2 (EC 3.5.1.98) | protein | 366 | 40% helix, 13% strand | Q92769 |
Ligands and binding sites
- V1S · (1S)-N-{(1S)-1-[5-cyano-2-(4-fluorophenyl)-1H-imidazol-4-yl]-7,7-dihydroxynonyl}-6-methyl-6-azaspiro[2.5]octane-1-carboxamide · ligand · 3 copies · chains A, B, C
- CA · Calcium ion · metal · 6 copies · chains A, B, C
- ZN · Zinc ion · metal · 3 copies · chains A, B, C
- SO4 · Sulfate ion · ion · 10 copies · chains A, B, C
- PEG · Di(hydroxyethyl)ether · additive · 7 copies · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 756 | 0.72 | 0.78 | 76 | SO4 |
| 2 | 545 | 0.63 | 0.75 | 57 | empty |
| 3 | 220 | 0.52 | 0.77 | 21 | SO4 |
| 4 | 51 | 0.46 | 0.85 | 19 | ZN, V1S |
| 5 | 52 | 0.46 | 0.85 | 18 | V1S |
Interfaces
3 interfaces between chains.
- A–C · 611 Ų buried · 11 hydrogen bonds · protein-protein
- A–B · 557 Ų buried · 13 hydrogen bonds · protein-protein
- B–C · 357 Ų buried · 4 hydrogen bonds · protein-protein
Compared structures
- 6XEC · Structure of human HDAC2 in complex with ketone inhibitor (compound O) · the same entry in another collection · chain A against A, TM-score 1.00
- Q92769 · AlphaFold monomer V2.0 prediction for histone deacetylase 2 (Q92769) · a predicted model of the same protein · chain B 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 Q92769
- Elsewhere: RCSB PDB 6XEC · PDBe 6XEC · UniProt Q92769
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