Research workbench
HDAC7 bound with tfmo inhibitor TMP942
Analyse HDAC7 bound with tfmo inhibitor TMP942 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3ZNS
- Type
- protein
- Length
- 1,107 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Histone deacetylase 7
- EC
- 3.5.1.98
- UniProt
- Q8WUI4
- Ligands
- NU7, ZN, K
- Pockets
- 9 · best druggability 0.61
Structure
x-ray diffraction · 3 distinct chains · 40% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Histone deacetylase 7 (EC 3.5.1.98) | protein | 368 | 39% helix, 14% strand | Q8WUI4 |
| B | Histone deacetylase 7 (EC 3.5.1.98) | protein | 380 | 41% helix, 14% strand | Q8WUI4 |
| C | Histone deacetylase 7 (EC 3.5.1.98) | protein | 359 | 41% helix, 14% strand | Q8WUI4 |
Ligands and binding sites
- NU7 · N-{[1-methyl-4-(4-phenyl-1,3-thiazol-2-yl)piperidin-4-yl]methyl}-3-[5-(trifluoromethyl)-1,2,4-oxadiazol-3-yl]benzamide · ligand · 3 copies · chains A, B, C
- ZN · Zinc ion · metal · 6 copies · chains A, B, C
- K · Potassium ion · metal · 6 copies · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 153 | 0.61 | 0.84 | 22 | NU7 |
| 2 | 134 | 0.59 | 0.84 | 24 | NU7 |
| 3 | 161 | 0.59 | 0.83 | 24 | NU7 |
| 4 | 267 | 0.53 | 0.76 | 35 | empty |
| 5 | 305 | 0.52 | 0.74 | 39 | empty |
Interfaces
3 interfaces between chains.
- A–B · 490 Ų buried · 6 hydrogen bonds · protein-protein
- B–C · 233 Ų buried · 2 hydrogen bonds · protein-protein
- A–C · 48 Ų buried · 0 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 Q8WUI4
- Elsewhere: RCSB PDB 3ZNS · PDBe 3ZNS · UniProt Q8WUI4
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