Research workbench
Factor viia in complex with the inhibitor 4-{[(R)-[5-ethoxy-2-fluoro- 3-(propan-2-YLOXY)PHENYL](4-phenyl-1H-imidazol-2-yl) METHYL]AMINO}BENZENECARBOXIMIDAMIDE
Analyse Factor viia in complex with the inhibitor 4-{[(R)-[5-ethoxy-2-fluoro… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4YT6
- Type
- protein
- Length
- 309 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Coagulation factor VII (heavy chain); Coagulation factor VII (light chain)
- EC
- 3.4.21.21
- UniProt
- P08709
- Ligands
- 4JY, CA, SO4
- Pockets
- 3 · best druggability 0.47
Structure
x-ray diffraction · 2 distinct chains · 15% helix, 35% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| H | Coagulation factor VII (heavy chain) (EC 3.4.21.21) | protein | 254 | 15% helix, 37% strand | P08709 |
| L | Coagulation factor VII (light chain) (EC 3.4.21.21) | protein | 55 | 15% helix, 25% strand | P08709 |
Ligands and binding sites
- 4JY · 4-[[(R)-(5-ethoxy-2-fluoranyl-3-propan-2-yloxy-phenyl)-(4-phenyl-1H-imidazol-2-yl)methyl]amino]benzenecarboximidamide · 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
3 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 62 | 0.47 | 0.84 | 17 | SO4 |
| 2 | 124 | 0.41 | 0.75 | 26 | 4JY |
| 3 | 98 | 0.37 | 0.75 | 15 | SO4 |
Interfaces
1 interface between chains.
- H–L · 1029 Ų buried · 13 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 disulfide (disulfide).
Compared structures
- 4YT6 · Factor VIIa in complex with the inhibitor 4-{[(R)-[5-ethoxy-2-fluoro-3-(propan-2-yloxy)phe… · 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 4YT6 · PDBe 4YT6 · UniProt P08709
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