Research workbench
Thrombin inhibitors
Analyse Thrombin inhibitors in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2C8X
- Type
- protein
- Length
- 290 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Thrombin light chain; Thrombin heavy chain; Hirudin variant-2
- EC
- 3.4.21.5
- UniProt
- P00734, P09945
- Ligands
- C5M, NA
- Pockets
- 4 · best druggability 0.56
Structure
x-ray diffraction · 3 distinct chains · 17% helix, 30% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Thrombin light chain (EC 3.4.21.5) | protein | 29 | 34% helix, 0% strand | P00734 |
| B | Thrombin heavy chain (EC 3.4.21.5) | protein | 251 | 14% helix, 35% strand | P00734 |
| I | Hirudin variant-2 | protein | 10 | 30% helix, 0% strand | P09945 |
Ligands and binding sites
- C5M · N-{(2R,3S)-3-[(3-chlorobenzyl)amino]-2-hydroxy-4-phenylbutyl}-4-methoxy-2,3,6-trimethylbenzenesulfonamide · ligand · chains B
- NA · Sodium ion · metal · chains B
- DMS · Dimethyl sulfoxide · additive · 2 copies · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 259 | 0.56 | 0.77 | 39 | C5M |
| 2 | 86 | 0.38 | 0.76 | 16 | empty |
| 3 | 50 | 0.32 | 0.78 | 14 | empty |
| 4 | 52 | 0.29 | 0.75 | 12 | empty |
Interfaces
2 interfaces between chains.
- A–B · 1205 Ų buried · 28 hydrogen bonds · protein-protein
- B–I · 630 Ų buried · 7 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide, 1 modified (disulfide, sulfation).
Compared structures
- 2C8X · 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 P09945
- Elsewhere: RCSB PDB 2C8X · PDBe 2C8X · UniProt P00734 · UniProt P09945
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.