MolNFT v1 · #182377 · protein
Structure of HDAC2 in complex with an inhibitor (compound 19)
7MOY · Histone deacetylase 2: “Structure of HDAC2 in complex with an inhibitor (compound 19)”. X-ray diffraction, 4 ligands (ZLM, CA, ZN), 4 pockets (best druggability 0.73). MolNFT v1 #182377 on GenesisL1: 3D structure, binding sites and…
- PDB
- 7MOY
- 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
- ZLM, CA, ZN, SO4
- Pockets
- 4 · best druggability 0.73
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 | 41% helix, 13% strand | Q92769 |
| C | Histone deacetylase 2 (EC 3.5.1.98) | protein | 368 | 40% helix, 13% strand | Q92769 |
Ligands and binding sites
- ZLM · (1S)-6-ethyl-N-{(1S)-1-[5-(2-ethyl-1-oxo-1,2-dihydroisoquinolin-6-yl)-1H-imidazol-2-yl]-7,7-dihydroxynonyl}-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
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 | 759 | 0.73 | 0.78 | 72 | SO4 |
| 2 | 535 | 0.64 | 0.76 | 52 | empty |
| 3 | 226 | 0.54 | 0.78 | 21 | SO4 |
| 4 | 51 | 0.45 | 0.84 | 19 | ZLM |
Interfaces
3 interfaces between chains.
- A–C · 603 Ų buried · 11 hydrogen bonds · protein-protein
- A–B · 553 Ų buried · 13 hydrogen bonds · protein-protein
- B–C · 356 Ų buried · 5 hydrogen bonds · protein-protein
Compared structures
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 7MOY · PDBe 7MOY · UniProt Q92769
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