MolNFT v1 · #168311 · protein
Structure of human HDAC2 in complex with an ethyl ketone inhibitor containing a spiro-bicyclic group
6WBZ · Histone deacetylase 2: “Structure of human HDAC2 in complex with an ethyl ketone inhibitor containing a spiro-bicyclic group”. X-ray diffraction, 4 ligands (TV7, CA, ZN), 3 pockets (best druggability 0.73). MolNFT v1 #168311 on…
- PDB
- 6WBZ
- Type
- protein
- Length
- 1,101 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
- TV7, CA, ZN, SO4
- Pockets
- 3 · best druggability 0.73
Structure
x-ray diffraction · 3 distinct chains · 41% 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 | 367 | 41% helix, 13% strand | Q92769 |
Ligands and binding sites
- TV7 · (1S)-N-{(1S)-7,7-dihydroxy-1-[5-(2-methoxyquinolin-3-yl)-1H-imidazol-2-yl]nonyl}-6-ethyl-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
3 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 808 | 0.73 | 0.78 | 75 | SO4 |
| 2 | 515 | 0.64 | 0.76 | 45 | empty |
| 3 | 241 | 0.55 | 0.78 | 22 | SO4 |
Interfaces
3 interfaces between chains.
- A–C · 626 Ų buried · 12 hydrogen bonds · protein-protein
- A–B · 546 Ų buried · 14 hydrogen bonds · protein-protein
- B–C · 356 Ų buried · 5 hydrogen bonds · protein-protein
Compared structures
- 6WBZ · Structure of Human HDAC2 in complex with an ethyl ketone inhibitor containing a… · 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 6WBZ · PDBe 6WBZ · UniProt Q92769
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