Research workbench
Crystal structure of small molecule inhibitor TM5484 bound to stabilized active plasminogen activator inhibitor-1 (pai-1-W175F)
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
- 7AQG
- Type
- protein
- Length
- 597 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Plasminogen activator inhibitor 1; Vhh-2G-42 (NB42); Vhh-2W-64 (NB64)
- UniProt
- P05121
- Ligands
- RV2
- Pockets
- 2 · best druggability 0.58
Structure
x-ray diffraction · 3 distinct chains · 19% helix, 40% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Plasminogen activator inhibitor 1 | protein | 362 | 30% helix, 32% strand | P05121 |
| B | Vhh-2G-42 (NB42) | protein | 114 | 5% helix, 53% strand | — |
| C | Vhh-2W-64 (NB64) | protein | 121 | 2% helix, 51% strand | — |
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
2 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 288 | 0.58 | 0.78 | 33 | empty |
| 2 | 169 | 0.58 | 0.82 | 23 | empty |
Interfaces
2 interfaces between chains.
- A–C · 838 Ų buried · 14 hydrogen bonds · protein-protein
- A–B · 639 Ų buried · 7 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 disulfide (disulfide).
Compared structures
- 7AQG · 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 0.99
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 7AQG · PDBe 7AQG · UniProt P05121
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.