MolNFT v1 · #16653 · protein
Dissecting and designing inhibitor selectivity determinants at the S1 site using an artificial ALA190 protease (ALA190 upa)
1O5D · Coagulation factor VII: “Dissecting and designing inhibitor selectivity determinants at the S1 site using an artificial ALA190…”. X-ray diffraction, 1 ligand (CR9), 8 pockets (best druggability 0.69). MolNFT v1 #16653 on GenesisL1…
- PDB
- 1O5D
- Type
- protein
- Length
- 501 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
- CR9
- Pockets
- 8 · best druggability 0.69
Structure
x-ray diffraction · 3 distinct chains · 12% helix, 38% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| L | Coagulation factor VII (EC 3.4.21.21) | protein | 96 | 14% helix, 30% strand | P08709 |
| H | Coagulation factor VII (EC 3.4.21.21) | protein | 254 | 13% helix, 37% strand | P08709 |
| T | Tissue factor | protein | 151 | 9% helix, 45% strand | P13726 |
Ligands and binding sites
- CR9 · 2-{5-[amino(iminio)methyl]-6-fluoro-1H-benzimidazol-2-yl}-6-[(2-methylcyclohexyl)oxy]benzenolate · ligand · chains H
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 323 | 0.69 | 0.83 | 48 | empty |
| 2 | 149 | 0.45 | 0.76 | 22 | empty |
| 3 | 64 | 0.45 | 0.82 | 17 | empty |
| 4 | 139 | 0.44 | 0.76 | 20 | empty |
| 5 | 95 | 0.44 | 0.79 | 25 | empty |
Interfaces
3 interfaces between chains.
- L–H · 1006 Ų buried · 13 hydrogen bonds · protein-protein
- L–T · 893 Ų buried · 12 hydrogen bonds · protein-protein
- H–T · 689 Ų buried · 14 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 12 disulfide (disulfide).
Compared structures
- 1O5D · Dissecting and Designing Inhibitor Selectivity Determinants at the S1 site Using an… · the same entry in another collection · chain L against L, 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
- 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
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 1O5D · PDBe 1O5D · UniProt P08709 · UniProt P13726
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