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Structural basis for selectivity of a small molecule, S1-binding, sub- micromolar inhibitor of urokinase type plasminogen activator
Analyse Structural basis for selectivity of a small molecule, S1-binding, sub… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1C5Y
- Type
- protein
- Length
- 257 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Protein (urokinase-type plasminogen activator)
- EC
- 3.4.21.73
- UniProt
- P00749
- Ligands
- ESP
- Pockets
- 1 · best druggability 0.40
Structure
x-ray diffraction · 2 distinct chains · 10% helix, 40% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Protein (urokinase-type plasminogen activator) (EC 3.4.21.73) | protein | 9 | 0% helix, 0% strand | P00749 |
| B | Protein (urokinase-type plasminogen activator) (EC 3.4.21.73) | protein | 248 | 10% helix, 41% strand | P00749 |
Ligands and binding sites
- ESP · Thieno[2,3-b]pyridine-2-carboxamidine · ligand · chains B
- FLC · Citrate anion · additive · 3 copies · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
1 pocket found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 110 | 0.40 | 0.76 | 26 | FLC, ESP |
Interfaces
1 interface between chains.
- A–B · 555 Ų buried · 7 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 disulfide (disulfide).
Compared structures
- 1C5Y · Structural basis for selectivity of a small molecule, S1-binding, sub-micromolar… · the same entry in another collection · chain B against B, 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 1C5Y · PDBe 1C5Y · UniProt P00749
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