MolNFT v1 · #111130 · protein
Reversal agent for dabigatran
4YHI · Adabi-FAB2A heavy chain: “Reversal agent for dabigatran”. X-ray diffraction, 1 ligand (4CC), 12 pockets (best druggability 0.82). MolNFT v1 #111130 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 4YHI
- Type
- protein
- Length
- 882 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Adabi-FAB2A heavy chain; Adabi-FAB2A light chain
- Ligands
- 4CC
- Pockets
- 12 · best druggability 0.82
Structure
x-ray diffraction · 2 distinct chains · 7% helix, 50% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, H | Adabi-FAB2A heavy chain | protein | 222 | 8% helix, 50% strand | — |
| B, L | Adabi-FAB2A light chain | protein | 219 | 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 · 2 copies · chains A, B, H, L
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 933 | 0.82 | 0.84 | 88 | empty |
| 2 | 512 | 0.73 | 0.82 | 80 | empty |
| 3 | 222 | 0.73 | 0.88 | 41 | empty |
| 4 | 251 | 0.69 | 0.85 | 50 | empty |
| 5 | 275 | 0.61 | 0.80 | 29 | empty |
Interfaces
6 interfaces between chains.
- A–B · 2054 Ų buried · 22 hydrogen bonds · protein-protein
- H–L · 2042 Ų buried · 22 hydrogen bonds · protein-protein
- A–H · 610 Ų buried · 6 hydrogen bonds · protein-protein
- B–H · 557 Ų buried · 6 hydrogen bonds · protein-protein
- A–L · 110 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 10 disulfide (disulfide).
Compared structures
- 4YHI · Reversal Agent 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 4YHI · PDBe 4YHI
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