MolNFT v1 · #69428 · protein
Factor xa in complex with the inhibitor N-(3-fluoro-2'- (METHYLSULFONYL)BIPHENYL-4-yl)-1-(3-(5-oxo-4,5-dihydro-1H- 1,2,4- triazol-3-YL)PHENYL)-3-(trifluoromethyl)-1H- pyrazole-5-carboxamide
3KQB · Factor xa heavy chain: “Factor xa in complex with the inhibitor N-(3-fluoro-2'- (METHYLSULFONYL)BIPHENYL-4-yl)-1-(3-(5-oxo-4,5-dihydro…”. X-ray diffraction, 2 ligands (LGJ, NA), 2 pockets (best druggability 0.50). MolNFT v1 #69428…
- PDB
- 3KQB
- 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
- LGJ, NA
- Pockets
- 2 · best druggability 0.50
Structure
x-ray diffraction · 2 distinct chains · 13% helix, 36% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Factor xa heavy chain (EC 3.4.21.6) | protein | 234 | 13% helix, 37% strand | P00742 |
| L | Factor xa light chain (EC 3.4.21.6) | protein | 52 | 13% helix, 31% strand | P00742 |
Ligands and binding sites
- LGJ · N-(3-fluoro-2'-(methylsulfonyl)biphenyl-4-yl)-1-(3-(5-oxo-4,5-dihydro-1H-1,2,4-triazol-3-yl)phenyl)-3-(trifluoromethyl)-1H-pyrazole-5-carboxamide · 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 | 0.50 | 0.78 | 35 | LGJ |
| 2 | 160 | 0.44 | 0.75 | 27 | empty |
Interfaces
1 interface between chains.
- A–L · 939 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 3KQB · PDBe 3KQB · UniProt P00742
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