Research workbench
Design and discovery of novel, potent thrombin inhibitors with a solubilizing cationic P1-P2-linker
Analyse Design and discovery of novel, potent thrombin inhibitors with a solubilizing… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2BXU
- Type
- protein
- Length
- 289 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Alpha thrombin; Hirudin
- EC
- 3.4.21.5
- UniProt
- P00734, P09945
- Ligands
- C1D
- Pockets
- 2 · best druggability 0.57
Structure
x-ray diffraction · 3 distinct chains · 17% helix, 30% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| H | Alpha thrombin (EC 3.4.21.5) | protein | 251 | 14% helix, 35% strand | P00734 |
| I | Hirudin | protein | 11 | 27% helix, 0% strand | P09945 |
| L | Alpha thrombin (EC 3.4.21.5) | protein | 27 | 37% helix, 0% strand | P00734 |
Ligands and binding sites
- C1D · 1-(2-{[(6-amino-2-methylpyridin-3-yl)methyl]amino}ethyl)-6-chloro-3-[(2,2-difluoro-2-pyridin-2-ylethyl)amino]-1,4-dihydropyrazin-2-ol · ligand · chains H
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 | 246 | 0.57 | 0.78 | 40 | C1D |
| 2 | 71 | 0.35 | 0.76 | 16 | empty |
Interfaces
2 interfaces between chains.
- H–L · 1119 Ų buried · 24 hydrogen bonds · protein-protein
- H–I · 669 Ų buried · 9 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide, 1 modified (disulfide, sulfation).
Compared structures
- 2BXU · Design and Discovery of Novel, Potent Thrombin Inhibitors with a Solubilizing Cationic… · the same entry in another collection · chain H against H, 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 2BXU · PDBe 2BXU · UniProt P00734 · UniProt P09945
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