MolNFT v1 · #109641 · protein
Factor viia in complex with the inhibitor (methyl {3-[(2R)-1-{(2R)-2- (3,4-dimethoxyphenyl)-2-[(1-oxo-1,2,3,4-tetrahydroisoquinolin-7-yl) AMINO]ACETYL}PYRROLIDIN-2-yl]-4-(propan-2-ylsulfonyl) PHENYL}CARBAMATE)
4X8V · Factor viia (heavy chain): “Factor viia in complex with the inhibitor (methyl {3-[(2R)-1-{(2R)-2…”. X-ray diffraction, 3 ligands (3Z9, CA, SO4), 3 pockets (best druggability 0.49). MolNFT v1 #109641 on GenesisL1: 3D structure…
- PDB
- 4X8V
- 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
- 3Z9, CA, SO4
- Pockets
- 3 · best druggability 0.49
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) (EC 3.4.21.21) | protein | 55 | 15% helix, 25% strand | P08709 |
Ligands and binding sites
- 3Z9 · methyl {3-[(2R)-1-{(2R)-2-(3,4-dimethoxyphenyl)-2-[(1-oxo-1,2,3,4-tetrahydroisoquinolin-7-yl)amino]acetyl}pyrrolidin-2-yl]-4-(propan-2-ylsulfonyl)phenyl}carbamate · ligand · chains H
- CA · Calcium ion · metal · chains H
- SO4 · Sulfate ion · ion · 3 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 | 66 | 0.49 | 0.84 | 17 | empty |
| 2 | 136 | 0.44 | 0.76 | 31 | 3Z9 |
| 3 | 116 | 0.40 | 0.75 | 20 | SO4 |
Interfaces
1 interface between chains.
- H–L · 1050 Ų buried · 13 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 disulfide (disulfide).
Compared structures
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 4X8V · PDBe 4X8V · UniProt P08709
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