Research workbench
Factor xa in complex with the inhibitor 1-[2-(aminomethyl) phenyl]-N-(3-fluoro-2'-sulfamoylbiphenyl-4-yl)-3- (trifluoromethyl)-1H-pyrazole-5-carboxamide (DPC602)
Analyse Factor xa in complex with the inhibitor 1-[2-(aminomethyl)… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3M37
- Type
- protein
- Length
- 286 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Coagulation factor X
- EC
- 3.4.21.6
- UniProt
- P00742
- Ligands
- M37, CA
- Pockets
- 2 · best druggability 0.48
Structure
x-ray diffraction · 2 distinct chains · 13% helix, 35% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Coagulation factor X (EC 3.4.21.6) | protein | 234 | 13% helix, 36% strand | P00742 |
| L | Coagulation factor X (EC 3.4.21.6) | protein | 52 | 13% helix, 31% strand | P00742 |
Ligands and binding sites
- M37 · 1-[2-(aminomethyl)phenyl]-N-(3-fluoro-2'-sulfamoylbiphenyl-4-yl)-3-(trifluoromethyl)-1H-pyrazole-5-carboxamide · 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 | 122 | 0.48 | 0.79 | 29 | M37 |
| 2 | 90 | 0.37 | 0.75 | 19 | empty |
Interfaces
1 interface between chains.
- A–L · 950 Ų buried · 9 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 disulfide (disulfide).
Compared structures
- 3M37 · Factor XA in complex with the inhibitor 1-[2-(aminomethyl)phenyl]-N-(3-fluoro-2'-sulfamoyl… · the same entry in another collection · chain A against A, TM-score 1.00
- P00742 · AlphaFold monomer V2.0 prediction for coagulation factor X (P00742) · a predicted model of the same protein · chain A against A, TM-score 0.99
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 3M37 · PDBe 3M37 · UniProt P00742
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