Research workbench
Active site thrombin inhibitors
Analyse 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
- 1WBG
- Type
- protein
- Length
- 292 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Thrombin light chain; Thrombin heavy chain; Hirugen
- EC
- 3.4.21.5
- UniProt
- P00734, P09945
- Ligands
- L03
- Pockets
- 2 · best druggability 0.58
Structure
x-ray diffraction · 3 distinct chains · 18% helix, 30% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Thrombin light chain (EC 3.4.21.5) | protein | 31 | 32% helix, 0% strand | P00734 |
| B | Thrombin heavy chain (EC 3.4.21.5) | protein | 251 | 16% helix, 35% strand | P00734 |
| I | Hirugen | protein | 10 | 30% helix, 0% strand | P09945 |
Ligands and binding sites
- L03 · 3-(4-chlorophenyl)-5-(methylthio)-4H-1,2,4-triazole · ligand · chains B
- DMS · Dimethyl sulfoxide · additive · 3 copies · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 281 | 0.58 | 0.78 | 38 | L03, DMS |
| 2 | 76 | 0.35 | 0.76 | 14 | empty |
Interfaces
2 interfaces between chains.
- A–B · 1227 Ų buried · 31 hydrogen bonds · protein-protein
- B–I · 644 Ų buried · 6 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide, 1 modified (disulfide, sulfation).
Compared structures
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 P09945
- Elsewhere: RCSB PDB 1WBG · PDBe 1WBG · UniProt P00734 · UniProt P09945
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