Research workbench
Fragment-based discovery of mexiletine derivatives as orally bioavailable inhibitors of urokinase-type plasminogen activator
Analyse Fragment-based discovery of mexiletine derivatives as orally bioavailable… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2VIP
- Type
- protein
- Length
- 247 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Urokinase-type plasminogen activator chain B
- EC
- 3.4.21.73
- UniProt
- P00749
- Ligands
- L1R, SO4
- Pockets
- 2 · best druggability 0.44
Structure
x-ray diffraction · 1 distinct chain · 11% helix, 39% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Urokinase-type plasminogen activator chain B (EC 3.4.21.73) | protein | 247 | 11% helix, 39% strand | P00749 |
Ligands and binding sites
- L1R · 4-(2-aminoethoxy)-3,5-dichloro-N-[3-(1-methylethoxy)phenyl]benzamide · ligand · chains A
- SO4 · Sulfate ion · ion · chains A
- ACT · Acetate ion · additive · 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, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 180 | 0.44 | 0.75 | 33 | ACT, L1R |
| 2 | 53 | 0.35 | 0.79 | 14 | empty |
Modifications
Observed in the structure: 5 disulfide (disulfide).
Compared structures
- 2VIP · Fragment-Based Discovery of Mexiletine Derivatives as Orally Bioavailable Inhibitors of… · 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 2VIP · PDBe 2VIP · UniProt P00749
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