Research workbench
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
- 1C5N
- Type
- protein
- Length
- 298 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Thrombin light chain; Thrombin heavy chain; Hirudin
- EC
- 3.4.21.5
- UniProt
- P00734, P28504
- Ligands
- ESI, NA, CA
- Pockets
- 3 · best druggability 0.53
Structure
x-ray diffraction · 3 distinct chains · 17% helix, 30% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| L | Thrombin light chain (EC 3.4.21.5) | protein | 36 | 28% helix, 6% strand | P00734 |
| H | Thrombin heavy chain (EC 3.4.21.5) | protein | 252 | 15% helix, 34% strand | P00734 |
| I | Hirudin | protein | 10 | 30% helix, 0% strand | P28504 |
Ligands and binding sites
- ESI · 4-iodobenzo[b]thiophene-2-carboxamidine · ligand · chains H
- NA · Sodium ion · metal · chains H
- CA · Calcium ion · metal · chains H
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 246 | 0.53 | 0.76 | 34 | ESI |
| 2 | 51 | 0.30 | 0.76 | 16 | empty |
| 3 | 57 | 0.30 | 0.75 | 12 | empty |
Interfaces
2 interfaces between chains.
- L–H · 1398 Ų buried · 32 hydrogen bonds · protein-protein
- H–I · 668 Ų buried · 8 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide, 1 modified (disulfide, sulfation).
Compared structures
- 1C5N · Structural basis for selectivity of a small molecule, S1-binding, sub-micromolar… · the same entry in another collection · chain L against L, TM-score 1.00
- P28504 · AlphaFold monomer V2.0 prediction for hirudin-2 (P28504) · a predicted model of the same protein · chain I against A, TM-score 0.51
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 P00734
- Every structure of UniProt P28504
- Elsewhere: RCSB PDB 1C5N · PDBe 1C5N · UniProt P00734 · UniProt P28504
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