Research workbench
Reversal agent for dabigatran
Analyse Reversal agent for dabigatran in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4YHK
- Type
- protein
- Length
- 440 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Adabi-FAB2A heavy chain; Adabi-FAB2A light chain
- Ligands
- 4CC
- Pockets
- 5 · best druggability 0.65
Structure
x-ray diffraction · 2 distinct chains · 6% helix, 51% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| H | Adabi-FAB2A heavy chain | protein | 222 | 7% helix, 51% strand | — |
| L | Adabi-FAB2A light chain | protein | 218 | 5% helix, 50% 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 · chains H, L
- GOL · Glycerol · additive · 2 copies · chains H, L
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 671 | 0.65 | 0.75 | 60 | GOL |
| 2 | 77 | 0.43 | 0.80 | 26 | 4CC |
| 3 | 58 | 0.38 | 0.80 | 15 | empty |
| 4 | 71 | 0.32 | 0.75 | 17 | empty |
| 5 | 72 | 0.31 | 0.74 | 18 | empty |
Interfaces
1 interface between chains.
- H–L · 2080 Ų buried · 21 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide (disulfide).
Compared structures
- 4YHK · Reversal Agent for Dabigatran · 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
- Elsewhere: RCSB PDB 4YHK · PDBe 4YHK
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