Research workbench
Factor xa in complex with the inhibitor 1-(3-(5-oxo-4,5- dihydro-1H-1, 2,4-triazol-3-YL)PHENYL)-6-(2'-(pyrrolidin-1- YLMETHYL)BIPHENYL-4- yl)-3-(trifluoromethyl)-5,6-dihydro- 1H-PYRAZOLO[3,4-C]PYRIDIN-7(4H)- one
Analyse Factor xa in complex with the inhibitor 1-(3-(5-oxo-4,5- dihydro-1H-1… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3KQD
- Type
- protein
- Length
- 286 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Factor xa heavy chain; Factor xa light chain
- EC
- 3.4.21.6
- UniProt
- P00742
- Ligands
- LGL, NA
- Pockets
- 2 · best druggability 0.51
Structure
x-ray diffraction · 2 distinct chains · 14% helix, 34% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Factor xa heavy chain (EC 3.4.21.6) | protein | 234 | 14% helix, 35% strand | P00742 |
| L | Factor xa light chain (EC 3.4.21.6) | protein | 52 | 13% helix, 31% strand | P00742 |
Ligands and binding sites
- LGL · 1-(3-(5-oxo-4,5-dihydro-1H-1,2,4-triazol-3-yl)phenyl)-6-(2'-(pyrrolidin-1-ylmethyl)biphenyl-4-yl)-3-(trifluoromethyl)-5,6-dihydro-1H-pyrazolo[3,4-c]pyridin-7(4H)-one · ligand · chains A
- NA · Sodium ion · metal · 2 copies · 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, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 160 | 0.51 | 0.79 | 37 | LGL |
| 2 | 143 | 0.45 | 0.76 | 26 | empty |
Interfaces
1 interface between chains.
- A–L · 942 Ų buried · 10 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 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 3KQD · PDBe 3KQD · UniProt P00742
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