Research workbench
Factor xia in complex with the inhibitor 1-{(1S)-1-[4-(3-amino-1H- indazol-6-yl)-5-chloro-1H-imidazol-2-yl]-2-phenylethyl}-3-[2- (aminomethyl)-5-CHLOROBENZYL]UREA
Analyse Factor xia in complex with the inhibitor 1-{(1S)-1-[4-(3-amino-1H… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4X6M
- Type
- protein
- Length
- 238 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Coagulation factor XI, light chain
- EC
- 3.4.21.27
- UniProt
- P03951
- Ligands
- 3Y3, SO4
- Pockets
- 2 · best druggability 0.42
Structure
x-ray diffraction · 1 distinct chain · 15% helix, 34% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Coagulation factor XI, light chain (EC 3.4.21.27) | protein | 238 | 15% helix, 34% strand | P03951 |
Ligands and binding sites
- 3Y3 · 1-{(1S)-1-[4-(3-amino-1H-indazol-6-yl)-5-chloro-1H-imidazol-2-yl]-2-phenylethyl}-3-[2-(aminomethyl)-5-chlorobenzyl]urea · ligand · chains A
- SO4 · Sulfate ion · ion · chains A
- EDO · 1,2-ethanediol · additive · 9 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, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 104 | 0.42 | 0.77 | 22 | empty |
| 2 | 122 | 0.42 | 0.76 | 23 | 3Y3, EDO |
Modifications
Observed in the structure: 4 disulfide (disulfide).
Compared structures
- 4X6M · FACTOR XIA IN COMPLEX WITH THE INHIBITOR 1-{(1S)-1-[4-(3-amino-1H-indazol-6-yl)-5-chloro-1… · the same entry in another collection · chain A against A, TM-score 1.00
- P03951 · AlphaFold monomer V2.0 prediction for coagulation factor XI (P03951) · a predicted model of the same protein · chain A against A, TM-score 0.98
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 P03951
- Elsewhere: RCSB PDB 4X6M · PDBe 4X6M · UniProt P03951
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