Research workbench
Factor xa in complex with the inhibitor 4-[(5-chloroindol-2-yl) sulfonyl]-2-(2-methylpropyl)-1-[[5-(pyridin-4-yl) pyrimidin-2- YL]CARBONYL]PIPERAZINE
Analyse Factor xa in complex with the inhibitor 4-[(5-chloroindol-2-yl)… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1WU1
- Type
- protein
- Length
- 287 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Coagulation factor X, heavy chain; Coagulation factor X, light chain
- EC
- 3.4.21.6
- UniProt
- P00742
- Ligands
- D91, 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, heavy chain (EC 3.4.21.6) | protein | 233 | 13% helix, 36% strand | P00742 |
| B | Coagulation factor X, light chain (EC 3.4.21.6) | protein | 54 | 13% helix, 30% strand | P00742 |
Ligands and binding sites
- D91 · 5-chloro-2-({3-isobutyl-4-[(5-pyridin-4-ylpyrimidin-2-yl)carbonyl]piperazin-1-yl}sulfonyl)-1H-indole · ligand · chains A
- CA · Calcium 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, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 114 | 0.48 | 0.80 | 26 | D91 |
| 2 | 105 | 0.37 | 0.74 | 27 | empty |
Interfaces
1 interface between chains.
- A–B · 862 Ų buried · 10 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 disulfide (disulfide).
Compared structures
- 1WU1 · Factor Xa in complex with the inhibitor 4-[(5-chloroindol-2-yl)sulfonyl]-2-(2-methylpropyl… · 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 1WU1 · PDBe 1WU1 · UniProt P00742
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.