MolNFT v1 · #111518 · protein
Factor viia in complex with the inhibitor 2-(2-{(R)-[(4- CARBAMIMIDOYLPHENYL)AMINO][5-ethoxy-2-fluoro-3-(propan-2-yloxy) PHENYL]METHYL}-1H-imidazol-4-YL)BENZAMIDE
4YT7 · Coagulation factor VII (heavy chain): “Factor viia in complex with the inhibitor 2-(2-{(R)-[(4…”. X-ray diffraction, 3 ligands (4K1, CA, SO4), 3 pockets (best druggability 0.45). MolNFT v1 #111518 on GenesisL1: 3D structure, binding…
- PDB
- 4YT7
- Type
- protein
- Length
- 311 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
- 4K1, CA, SO4
- Pockets
- 3 · best druggability 0.45
Structure
x-ray diffraction · 2 distinct chains · 15% helix, 34% 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 | 57 | 16% helix, 25% strand | P08709 |
Ligands and binding sites
- 4K1 · 2-[2-[(R)-[(4-carbamimidoylphenyl)amino]-(5-ethoxy-2-fluoranyl-3-propan-2-yloxy-phenyl)methyl]-1H-imidazol-4-yl]benzamide · ligand · chains H
- CA · Calcium ion · metal · chains H
- SO4 · Sulfate ion · ion · 4 copies · 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
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 | 80 | 0.45 | 0.81 | 17 | SO4 |
| 2 | 135 | 0.42 | 0.76 | 34 | 4K1, SO4 |
| 3 | 95 | 0.38 | 0.76 | 17 | SO4 |
Interfaces
1 interface between chains.
- H–L · 1020 Ų buried · 12 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 disulfide (disulfide).
Compared structures
- 4YT7 · Factor VIIa in complex with the inhibitor 2-(2-{(R)-[(4-carbamimidoylphenyl)amino][5-ethox… · 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 4YT7 · PDBe 4YT7 · UniProt P08709
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