MolNFT v1 · #28004 · protein
Crystal structure of ppar delta complexed with GW2331
1Y0S · Peroxisome proliferator activated receptor delta: “Crystal structure of ppar delta complexed with GW2331”. X-ray diffraction, 3 ligands (331, B7G, IOD), 5 pockets (best druggability 0.83). MolNFT v1 #28004 on GenesisL1: 3D…
- PDB
- 1Y0S
- Type
- protein
- Length
- 518 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Peroxisome proliferator activated receptor delta
- UniProt
- Q03181
- Ligands
- 331, B7G, IOD
- Pockets
- 5 · best druggability 0.83
Structure
x-ray diffraction · 2 distinct chains · 70% helix, 5% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Peroxisome proliferator activated receptor delta | protein | 260 | 70% helix, 5% strand | Q03181 |
| B | Peroxisome proliferator activated receptor delta | protein | 258 | 70% helix, 5% strand | Q03181 |
Ligands and binding sites
- 331 · (2S)-2-(4-[2-(3-[2,4-difluorophenyl]-1-heptylureido)ethyl]phenoxy)-2-methylbutyric acid · ligand · 2 copies · chains A, B
- B7G · heptyl beta-D-glucopyranoside · ligand · 2 copies · chains A, B
- IOD · Iodide ion · ion · 11 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 532 | 0.83 | 0.89 | 60 | IOD, 331 |
| 2 | 525 | 0.82 | 0.88 | 57 | IOD, 331 |
| 3 | 121 | 0.50 | 0.80 | 17 | IOD |
| 4 | 85 | 0.39 | 0.77 | 17 | IOD |
| 5 | 71 | 0.35 | 0.76 | 13 | B7G |
Interfaces
1 interface between chains.
- A–B · 34 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 1Y0S · Crystal structure of PPAR delta complexed with GW2331 · the same entry in another collection · chain A against A, TM-score 1.00
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 Q03181
- Elsewhere: RCSB PDB 1Y0S · PDBe 1Y0S · UniProt Q03181
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