Research workbench
Discovery of tetrahydropyrimidin-2(1H)-one derivative tak-442: a potent, selective and orally active factor xa inhibitor
Analyse Discovery of tetrahydropyrimidin-2(1H)-one derivative tak-442: a potent… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3KL6
- Type
- protein
- Length
- 282 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
- 443, CA
- Pockets
- 3 · best druggability 0.50
Structure
x-ray diffraction · 2 distinct chains · 12% helix, 35% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Coagulation factor X heavy chain (EC 3.4.21.6) | protein | 232 | 13% helix, 36% strand | P00742 |
| B | Coagulation factor X light chain (EC 3.4.21.6) | protein | 50 | 8% helix, 32% strand | P00742 |
Ligands and binding sites
- 443 · 1-(1-{(2S)-3-[(6-chloronaphthalen-2-yl)sulfonyl]-2-hydroxypropanoyl}piperidin-4-yl)tetrahydropyrimidin-2(1H)-one · ligand · chains A
- CA · Calcium ion · metal · 3 copies · chains A, B
- EDO · 1,2-ethanediol · additive · 4 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 157 | 0.50 | 0.78 | 32 | 443 |
| 2 | 168 | 0.44 | 0.74 | 27 | empty |
| 3 | 102 | 0.39 | 0.75 | 17 | empty |
Interfaces
1 interface between chains.
- A–B · 845 Ų buried · 13 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 disulfide (disulfide).
Compared structures
- 3KL6 · Discovery of Tetrahydropyrimidin-2(1H)-one derivative TAK-442: A potent, selective and… · 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 3KL6 · PDBe 3KL6 · UniProt P00742
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