Research workbench
Structure of human HDAC2 in complex with ketone inhibitor (compound E)
Analyse Structure of human HDAC2 in complex with ketone inhibitor (compound E) in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6XEB
- Type
- protein
- Length
- 1,102 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
- V1P, CA, ZN, SO4
- Pockets
- 5 · best druggability 0.72
Structure
x-ray diffraction · 3 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 | 40% helix, 13% strand | Q92769 |
| B | Histone deacetylase 2 (EC 3.5.1.98) | protein | 366 | 40% helix, 13% strand | Q92769 |
| C | Histone deacetylase 2 (EC 3.5.1.98) | protein | 368 | 41% helix, 13% strand | Q92769 |
Ligands and binding sites
- V1P · 5-{(1S)-7,7-dihydroxy-1-[(1-methylazetidine-3-carbonyl)amino]nonyl}-2-phenyl-1H-imidazole-4-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
5 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 701 | 0.72 | 0.79 | 67 | SO4 |
| 2 | 466 | 0.62 | 0.76 | 37 | empty |
| 3 | 181 | 0.48 | 0.76 | 20 | SO4 |
| 4 | 53 | 0.44 | 0.83 | 19 | V1P |
| 5 | 56 | 0.26 | 0.73 | 18 | empty |
Interfaces
3 interfaces between chains.
- A–C · 624 Ų buried · 12 hydrogen bonds · protein-protein
- A–B · 535 Ų buried · 12 hydrogen bonds · protein-protein
- B–C · 360 Ų buried · 5 hydrogen bonds · protein-protein
Compared structures
- 6XEB · Structure of human HDAC2 in complex with ketone inhibitor (compound E) · 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 6XEB · PDBe 6XEB · UniProt Q92769
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