Research workbench
Factor viia in complex with the inhibitor (2R)-2-[(1-aminoisoquinolin- 6-YL)AMINO]-2-[3-ethoxy-4-(propan-2-YLOXY)PHENYL]-N-[2-(propan-2- YLSULFONYL)BENZYL]ETHANAMIDE
Analyse Factor viia in complex with the inhibitor (2R)-2-[(1-aminoisoquinolin… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4NGA
- Type
- protein
- Length
- 309 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Factor viia (heavy chain); Factor viia (light chain)
- EC
- 3.4.21.21
- UniProt
- P08709
- Ligands
- 2KF, CA, SO4
- Pockets
- 4 · best druggability 0.53
Structure
x-ray diffraction · 2 distinct chains · 15% helix, 35% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| H | Factor viia (heavy chain) (EC 3.4.21.21) | protein | 254 | 15% helix, 37% strand | P08709 |
| L | Factor viia (light chain) | protein | 55 | 15% helix, 25% strand | P08709 |
Ligands and binding sites
- 2KF · (2R)-2-[(1-aminoisoquinolin-6-yl)amino]-2-[3-ethoxy-4-(propan-2-yloxy)phenyl]-N-[2-(propan-2-ylsulfonyl)benzyl]ethanamide · ligand · chains H
- CA · Calcium ion · metal · chains H
- SO4 · Sulfate ion · ion · 4 copies · chains H, L
- GOL · Glycerol · additive · 3 copies · chains H, L
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 | 75 | 0.53 | 0.85 | 17 | SO4 |
| 2 | 134 | 0.45 | 0.77 | 30 | 2KF |
| 3 | 87 | 0.36 | 0.75 | 17 | SO4 |
| 4 | 61 | 0.29 | 0.74 | 14 | empty |
Interfaces
1 interface between chains.
- H–L · 1055 Ų buried · 13 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 disulfide (disulfide).
Compared structures
- 4NGA · Factor viia in complex with the inhibitor (2R)-2-[(1-aminoisoquinolin-6-yl)amino]-2-[3-eth… · the same entry in another collection · chain H against H, TM-score 1.00
- P08709 · AlphaFold monomer V2.0 prediction for coagulation factor VII (P08709) · a predicted model of the same protein · chain H against A, TM-score 0.97
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 P08709
- Elsewhere: RCSB PDB 4NGA · PDBe 4NGA · UniProt P08709
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