Research workbench
Tranexamic acid is an active site inhibitor of urokinase plasminogen activator
Analyse Tranexamic acid is an active site inhibitor of urokinase plasminogen activator in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6NMB
- Type
- protein
- Length
- 1,009 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Urokinase-type plasminogen activator
- EC
- 3.4.21.73
- UniProt
- P00749
- Ligands
- AMH, NO3
- Pockets
- 4 · best druggability 0.45
Structure
x-ray diffraction · 4 distinct chains · 10% helix, 36% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Urokinase-type plasminogen activator (EC 3.4.21.73) | protein | 251 | 10% helix, 37% strand | P00749 |
| B | Urokinase-type plasminogen activator (EC 3.4.21.73) | protein | 254 | 10% helix, 35% strand | P00749 |
| C | Urokinase-type plasminogen activator (EC 3.4.21.73) | protein | 253 | 10% helix, 36% strand | P00749 |
| D | Urokinase-type plasminogen activator (EC 3.4.21.73) | protein | 251 | 10% helix, 37% strand | P00749 |
Ligands and binding sites
- AMH · Trans-4-aminomethylcyclohexane-1-carboxylic acid · ligand · 4 copies · chains A, B, C, D
- NO3 · Nitrate ion · ion · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 145 | 0.45 | 0.77 | 33 | AMH |
| 2 | 116 | 0.44 | 0.78 | 25 | AMH |
| 3 | 83 | 0.41 | 0.79 | 25 | AMH |
| 4 | 115 | 0.39 | 0.75 | 31 | AMH |
Interfaces
1 interface between chains.
- A–B · 40 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 24 disulfide (disulfide).
Compared structures
- 6NMB · Tranexamic Acid is an Active Site Inhibitor of Urokinase Plasminogen Activator · the same entry in another collection · chain A against A, TM-score 1.00
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 P00749
- Elsewhere: RCSB PDB 6NMB · PDBe 6NMB · UniProt P00749
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