Research workbench
Crystal structure of small molecule inhibitor TM5484 bound to stabilized active plasminogen activator inhibitor-1 (pai-1-stab)
Analyse Crystal structure of small molecule inhibitor TM5484 bound to stabilized active… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7AQF
- Type
- protein
- Length
- 736 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Plasminogen activator inhibitor 1
- UniProt
- P05121
- Ligands
- RV2
- Pockets
- 9 · best druggability 0.69
Structure
x-ray diffraction · 2 distinct chains · 30% helix, 32% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Plasminogen activator inhibitor 1 | protein | 370 | 29% helix, 32% strand | P05121 |
| B | Plasminogen activator inhibitor 1 | protein | 366 | 31% helix, 32% strand | P05121 |
Ligands and binding sites
- RV2 · 5-Chloro-2-[[2-[3-(furan-3-yl)anilino]-2-oxoacetyl]amino]benzoic acid · ligand · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 543 | 0.69 | 0.79 | 43 | empty |
| 2 | 140 | 0.63 | 0.86 | 27 | empty |
| 3 | 86 | 0.59 | 0.87 | 19 | empty |
| 4 | 145 | 0.57 | 0.82 | 25 | empty |
| 5 | 232 | 0.53 | 0.77 | 41 | empty |
Interfaces
1 interface between chains.
- A–B · 814 Ų buried · 9 hydrogen bonds · protein-protein
Compared structures
- 7AQF · Crystal Structure of Small Molecule Inhibitor TM5484 Bound to Stabilized Active… · the same entry in another collection · chain A against A, TM-score 1.00
- P05121 · AlphaFold monomer V2.0 prediction for plasminogen activator inhibitor 1 (P05121) · a predicted model of the same protein · chain A against A, TM-score 0.97
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 P05121
- Elsewhere: RCSB PDB 7AQF · PDBe 7AQF · UniProt P05121
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