Research workbench
Crystal structure of the prostaglandin D2 receptor CRTH2 with fevipiprant
Analyse Crystal structure of the prostaglandin D2 receptor CRTH2 with fevipiprant in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6D26
- Type
- protein
- Length
- 447 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Prostaglandin D2 receptor 2, endolysin chimera
- UniProt
- Q9Y5Y4, D9IEF7
- Ligands
- FSY, OLA, SO4
- Pockets
- 4 · best druggability 0.76
Structure
x-ray diffraction · 1 distinct chain · 71% helix, 2% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Prostaglandin D2 receptor 2, endolysin chimera | protein | 447 | 71% helix, 2% strand | Q9Y5Y4, D9IEF7 |
Ligands and binding sites
- FSY · fevipiprant · ligand · chains A
- OLA · Oleic acid · ligand · chains A
- SO4 · Sulfate ion · ion · 9 copies · chains A
- SIN · Succinic acid · additive · 5 copies · chains A
- PGE · Triethylene glycol · additive · chains A
- PGO · S-1,2-propanediol · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 379 | 0.76 | 0.86 | 37 | FSY, SIN |
| 2 | 328 | 0.67 | 0.81 | 43 | SO4 |
| 3 | 119 | 0.46 | 0.78 | 21 | SO4 |
| 4 | 110 | 0.39 | 0.75 | 22 | SIN, PGO |
Modifications
Observed in the structure: 2 disulfide, 1 modified (disulfide, alkylation).
Compared structures
- 6D26 · Crystal structure of the prostaglandin D2 receptor CRTH2 with fevipiprant · the same entry in another collection · chain A against A, TM-score 1.00
- Q9Y5Y4 · AlphaFold monomer V2.0 prediction for prostaglandin D2 receptor 2 (Q9Y5Y4) · a predicted model of the same protein · chain A against A, TM-score 0.70
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 Q9Y5Y4
- Every structure of UniProt D9IEF7
- Elsewhere: RCSB PDB 6D26 · PDBe 6D26 · UniProt Q9Y5Y4 · UniProt D9IEF7
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