MolNFT v1 · #83758 · protein
The tuberculosis drug SQ109 inhibits trypanosoma cruzi cell proliferation and acts synergistically with posaconazole
3WSA · Squalene synthase: “The tuberculosis drug SQ109 inhibits trypanosoma cruzi cell proliferation and acts synergistically with…”. X-ray diffraction, 1 ligand (RWZ), 17 pockets (best druggability 0.81). MolNFT v1 #83758 on GenesisL1: 3D…
- 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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