Research workbench
Factor xia in complex with the inhibitor 4-(aminomethyl)-~{N}- [(1~{S})-1-[4-(3-oxidanyl-1~{H}-indazol-5-YL)PYRIDIN-2-yl]-2-phenyl- ETHYL]CYCLOHEXANE-1-carboxamide
Analyse Factor xia in complex with the inhibitor 4-(aminomethyl)-~{N}… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5EXL
- Type
- protein
- Length
- 238 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Coagulation factor xia light chain
- EC
- 3.4.21.27
- UniProt
- P03951
- Ligands
- 5SS, SO4
- Pockets
- 2 · best druggability 0.45
Structure
x-ray diffraction · 1 distinct chain · 15% helix, 34% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Coagulation factor xia light chain (EC 3.4.21.27) | protein | 238 | 15% helix, 34% strand | P03951 |
Ligands and binding sites
- 5SS · 4-(aminomethyl)-~{N}-[(1~{S})-1-[4-(3-oxidanyl-1~{H}-indazol-5-yl)pyridin-2-yl]-2-phenyl-ethyl]cyclohexane-1-carboxamide · ligand · chains A
- SO4 · Sulfate ion · ion · 2 copies · chains A
- EDO · 1,2-ethanediol · additive · 7 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 | 149 | 0.45 | 0.76 | 25 | 5SS |
| 2 | 111 | 0.42 | 0.77 | 18 | empty |
Modifications
Observed in the structure: 4 disulfide (disulfide).
Compared structures
- 5EXL · FACTOR XIA IN COMPLEX WITH THE INHIBITOR 4-(aminomethyl)-~{N}-[(1~{S})-1-[4-(3-oxidanyl-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 5EXL · PDBe 5EXL · UniProt P03951
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