Research workbench
The tuberculosis drug SQ109 inhibits trypanosoma cruzi cell proliferation and acts synergistically with posaconazole
Analyse The tuberculosis drug SQ109 inhibits trypanosoma cruzi cell proliferation and… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3WSA
- Type
- protein
- Length
- 1,976 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Squalene synthase
- EC
- 2.5.1.21
- UniProt
- P37268
- Ligands
- RWZ
- Pockets
- 17 · best druggability 0.81
Structure
x-ray diffraction · 6 distinct chains · 69% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Squalene synthase (EC 2.5.1.21) | protein | 329 | 69% helix, 0% strand | P37268 |
| B | Squalene synthase (EC 2.5.1.21) | protein | 332 | 69% helix, 0% strand | P37268 |
| C | Squalene synthase (EC 2.5.1.21) | protein | 332 | 69% helix, 0% strand | P37268 |
| D | Squalene synthase (EC 2.5.1.21) | protein | 325 | 68% helix, 0% strand | P37268 |
| E | Squalene synthase (EC 2.5.1.21) | protein | 330 | 69% helix, 0% strand | P37268 |
| F | Squalene synthase (EC 2.5.1.21) | protein | 328 | 70% helix, 0% strand | P37268 |
Ligands and binding sites
- RWZ · N-[(2Z)-3,7-dimethylocta-2,6-dien-1-yl]-N'-[(1R,3S,5R, 7R)-tricyclo[3.3.1.1~3,7~]dec-2-yl]ethane-1,2-diamine · ligand · 4 copies · chains A, B, C, E
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
17 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 843 | 0.81 | 0.83 | 61 | RWZ |
| 2 | 985 | 0.81 | 0.82 | 104 | empty |
| 3 | 826 | 0.80 | 0.83 | 60 | RWZ |
| 4 | 993 | 0.79 | 0.80 | 71 | RWZ |
| 5 | 934 | 0.79 | 0.81 | 65 | empty |
Interfaces
11 interfaces between chains.
- A–C · 1024 Ų buried · 7 hydrogen bonds · protein-protein
- E–F · 984 Ų buried · 5 hydrogen bonds · protein-protein
- D–E · 976 Ų buried · 9 hydrogen bonds · protein-protein
- A–B · 967 Ų buried · 5 hydrogen bonds · protein-protein
- B–C · 935 Ų buried · 5 hydrogen bonds · protein-protein
Compared structures
- 3WSA · The Tuberculosis Drug SQ109 Inhibits Trypanosoma cruzi Cell Proliferation and acts… · the same entry in another collection · chain F against F, TM-score 1.00
- P37268 · AlphaFold monomer V2.0 prediction for squalene synthase (P37268) · a predicted model of the same protein · chain A against A, TM-score 0.98
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 P37268
- Elsewhere: RCSB PDB 3WSA · PDBe 3WSA · UniProt P37268
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