Research workbench
An orally efficacious factor xa inhibitor
Analyse An orally efficacious factor xa inhibitor in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2PHB
- Type
- protein
- Length
- 285 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Coagulation factor X, heavy chain; Coagulation factor X, light chain
- EC
- 3.4.21.6
- UniProt
- P00742
- Ligands
- 230, CA
- Pockets
- 2 · best druggability 0.42
Structure
x-ray diffraction · 2 distinct chains · 9% helix, 34% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Coagulation factor X, heavy chain (EC 3.4.21.6) | protein | 234 | 11% helix, 37% strand | P00742 |
| B | Coagulation factor X, light chain (EC 3.4.21.6) | protein | 51 | 0% helix, 24% strand | P00742 |
Ligands and binding sites
- 230 · (2R,4R)-N~1~-(4-chlorophenyl)-N~2~-[2-fluoro-4-(2-oxopyridin-1(2H)-yl)phenyl]-4-methoxypyrrolidine-1,2-dicarboxamide · ligand · chains A
- CA · Calcium ion · metal · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 79 | 0.42 | 0.80 | 21 | 230 |
| 2 | 106 | 0.40 | 0.76 | 26 | empty |
Interfaces
1 interface between chains.
- A–B · 925 Ų buried · 13 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 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 P00742
- Elsewhere: RCSB PDB 2PHB · PDBe 2PHB · UniProt P00742
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