Research workbench
Novel covalent active site thrombin inhibitors
Analyse Novel covalent active site thrombin inhibitors in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1QJ6
- Type
- protein
- Length
- 305 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Thrombin; Hirugen
- EC
- 3.4.21.5
- UniProt
- P00734, P28501
- Ligands
- 167
- Pockets
- 3 · best druggability 0.60
Structure
x-ray diffraction · 3 distinct chains · 16% helix, 29% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Thrombin (EC 3.4.21.5) | protein | 36 | 25% helix, 0% strand | P00734 |
| B | Thrombin (EC 3.4.21.5) | protein | 259 | 15% helix, 34% strand | P00734 |
| I | Hirugen | protein | 10 | 30% helix, 0% strand | P28501 |
Ligands and binding sites
- 167 · 6-carbamimidoyl-2-[2-hydroxy-5-(3-methoxy-phenyl)-indan-1-yl]-hexanoic acid · ligand · chains B
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 | 277 | 0.60 | 0.79 | 43 | 167 |
| 2 | 95 | 0.41 | 0.77 | 16 | empty |
| 3 | 51 | 0.29 | 0.76 | 15 | empty |
Interfaces
2 interfaces between chains.
- A–B · 1210 Ų buried · 28 hydrogen bonds · protein-protein
- B–I · 629 Ų buried · 4 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide, 1 covalent, 1 modified (disulfide, covalent ligand, sulfation).
Compared structures
- 1QJ6 · Novel Covalent Active Site Thrombin Inhibitors · 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 P00734
- Every structure of UniProt P28501
- Elsewhere: RCSB PDB 1QJ6 · PDBe 1QJ6 · UniProt P00734 · UniProt P28501
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