Research workbench
Factor viia in complex with the inhibitor N-{3-[(2R)-1-{(2R)-2-[(1- aminoisoquinolin-6-YL)AMINO]-2-PHENYLACETYL}PYRROLIDIN-2-yl]-4- (propan-2-YLSULFONYL)PHENYL}ACETAMIDE
Analyse Factor viia in complex with the inhibitor N-{3-[(2R)-1-{(2R)-2-[(1… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4ZXX
- Type
- protein
- Length
- 309 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Coagulation factor viia heavy chain; Coagulation factor viia light chain
- EC
- 3.4.21.21
- UniProt
- P08709
- Ligands
- 4T0, CA, SO4
- Pockets
- 3 · best druggability 0.53
Structure
x-ray diffraction · 2 distinct chains · 14% helix, 34% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| H | Coagulation factor viia heavy chain (EC 3.4.21.21) | protein | 254 | 14% helix, 36% strand | P08709 |
| L | Coagulation factor viia light chain (EC 3.4.21.21) | protein | 55 | 15% helix, 25% strand | P08709 |
Ligands and binding sites
- 4T0 · N-{3-[(2R)-1-{(2R)-2-[(1-aminoisoquinolin-6-yl)amino]-2-phenylacetyl}pyrrolidin-2-yl]-4-(propan-2-ylsulfonyl)phenyl}acetamide · ligand · chains H
- CA · Calcium ion · metal · chains H
- SO4 · Sulfate ion · ion · 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, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 96 | 0.53 | 0.83 | 17 | empty |
| 2 | 100 | 0.41 | 0.77 | 25 | 4T0 |
| 3 | 88 | 0.37 | 0.76 | 15 | SO4 |
Interfaces
1 interface between chains.
- H–L · 1045 Ų buried · 13 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 disulfide (disulfide).
Compared structures
- 4ZXX · FACTOR VIIA IN COMPLEX WITH THE INHIBITOR N-{3-[(2R)-1-{(2R)-2-[(1-aminoisoquinolin-6-yl)a… · 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 4ZXX · PDBe 4ZXX · UniProt P08709
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