Research workbench
Low molecular weigth human urokinase type plasminogen activator 2-[6- (3'-aminomethyl-biphenyl-3-yloxy)-4-(3-dimethylamino-pyrrolidin-1- yl)-3,5-difluoro-pyridin-2-yloxy]-4-dimethylamino-benzoic acid complex
Analyse Low molecular weigth human urokinase type plasminogen activator 2-[6… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3IG6
- Type
- protein
- Length
- 500 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
- Q5SWW9
- Ligands
- 438, PO4
- Pockets
- 4 · best druggability 0.81
Structure
x-ray diffraction · 4 distinct chains · 11% helix, 38% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Urokinase-type plasminogen activator (EC 3.4.21.73) | protein | 3 | 0% helix, 0% strand | Q5SWW9 |
| B | Urokinase-type plasminogen activator (EC 3.4.21.73) | protein | 245 | 11% helix, 39% strand | Q5SWW9 |
| C | Urokinase-type plasminogen activator (EC 3.4.21.73) | protein | 9 | 0% helix, 0% strand | Q5SWW9 |
| D | Urokinase-type plasminogen activator (EC 3.4.21.73) | protein | 243 | 12% helix, 40% strand | Q5SWW9 |
Ligands and binding sites
- 438 · 2-[(6-{[3'-(aminomethyl)biphenyl-3-yl]oxy}-4-[(3R)-3-(dimethylamino)pyrrolidin-1-yl]-3,5-difluoropyridin-2-yl)oxy]-4-(dimethylamino)benzoic acid · ligand · 2 copies · chains B, D
- PO4 · Phosphate ion · ion · chains 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, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 595 | 0.81 | 0.86 | 52 | 438 |
| 2 | 691 | 0.75 | 0.80 | 74 | 438, PO4 |
| 3 | 109 | 0.47 | 0.79 | 20 | empty |
| 4 | 80 | 0.43 | 0.80 | 15 | empty |
Interfaces
3 interfaces between chains.
- B–D · 853 Ų buried · 12 hydrogen bonds · protein-protein
- C–D · 644 Ų buried · 10 hydrogen bonds · protein-protein
- A–B · 250 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 12 disulfide (disulfide).
Compared structures
- 3IG6 · Low molecular weigth human Urokinase type 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 Q5SWW9
- Elsewhere: RCSB PDB 3IG6 · PDBe 3IG6 · UniProt Q5SWW9
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