Research workbench
An antidote for dabigatran
Analyse An antidote for dabigatran in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4JN2
- Type
- protein
- Length
- 877 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Anti dabigatran Fab
- Ligands
- 4CC
- Pockets
- 11 · best druggability 0.68
Structure
x-ray diffraction · 3 distinct chains · 7% helix, 52% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, L | Anti dabigatran Fab | protein | 219 | 6% helix, 50% strand | — |
| B | Anti dabigatran Fab | protein | 214 | 7% helix, 52% strand | — |
| H | Anti dabigatran Fab | protein | 225 | 8% helix, 52% strand | — |
Ligands and binding sites
- 4CC · N-[(2-{[(4-carbamimidoylphenyl)amino]methyl}-1-methyl-1H-benzimidazol-5-yl)carbonyl]-N-pyridin-2-yl-beta-alanine · ligand · 2 copies · chains A, B, H, L
- GOL · Glycerol · additive · 8 copies · chains A, B, H, L
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 791 | 0.68 | 0.75 | 86 | empty |
| 2 | 780 | 0.67 | 0.75 | 69 | GOL |
| 3 | 56 | 0.53 | 0.89 | 22 | empty |
| 4 | 199 | 0.53 | 0.77 | 35 | empty |
| 5 | 228 | 0.51 | 0.76 | 24 | empty |
Interfaces
3 interfaces between chains.
- H–L · 2012 Ų buried · 18 hydrogen bonds · protein-protein
- A–B · 1849 Ų buried · 18 hydrogen bonds · protein-protein
- A–L · 533 Ų buried · 6 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 10 disulfide (disulfide).
Compared structures
- 4JN2 · An Antidote for Dabigatran · 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
- Elsewhere: RCSB PDB 4JN2 · PDBe 4JN2
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