Research workbench
Discovery of novel heterocyclic factor viia inhibitors
Analyse Discovery of novel heterocyclic factor viia inhibitors in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2F9B
- Type
- protein
- Length
- 497 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Coagulation factor VII; Tissue factor
- EC
- 3.4.21.21
- UniProt
- P08709, P13726
- Ligands
- N1H
- Pockets
- 7 · best druggability 0.73
Structure
x-ray diffraction · 3 distinct chains · 12% helix, 37% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| L | Coagulation factor VII (EC 3.4.21.21) | protein | 94 | 14% helix, 31% strand | P08709 |
| H | Coagulation factor VII (EC 3.4.21.21) | protein | 254 | 13% helix, 36% strand | P08709 |
| T | Tissue factor | protein | 149 | 11% helix, 44% strand | P13726 |
Ligands and binding sites
- N1H · {5-(5-amino-1H-pyrrolo[3,2-b]pyridin-2-yl)-6-hydroxy-3'-nitro-biphenyl-3-yl]-acetic acid · ligand · chains H
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 508 | 0.73 | 0.82 | 70 | empty |
| 2 | 142 | 0.50 | 0.79 | 24 | empty |
| 3 | 78 | 0.48 | 0.83 | 19 | empty |
| 4 | 137 | 0.44 | 0.76 | 23 | empty |
| 5 | 144 | 0.44 | 0.76 | 24 | N1H |
Interfaces
3 interfaces between chains.
- L–H · 966 Ų buried · 12 hydrogen bonds · protein-protein
- L–T · 878 Ų buried · 12 hydrogen bonds · protein-protein
- H–T · 664 Ų buried · 18 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 12 disulfide (disulfide).
Compared structures
- 2F9B · Discovery of Novel Heterocyclic Factor VIIa Inhibitors · the same entry in another collection · chain L against L, TM-score 1.00
- P13726 · AlphaFold monomer V2.0 prediction for tissue factor (P13726) · a predicted model of the same protein · chain T against A, TM-score 0.97
- 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
- Every structure of UniProt P13726
- Elsewhere: RCSB PDB 2F9B · PDBe 2F9B · UniProt P08709 · UniProt P13726
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