MolNFT v1 · #135600 · protein
Human ppardelta ligand-binding domain in complexed with specific agonist 6
5U3V · Peroxisome proliferator-activated receptor delta: “Human ppardelta ligand-binding domain in complexed with specific agonist 6”. X-ray diffraction, 2 ligands (B7G, 7TY), 4 pockets (best druggability 0.87). MolNFT v1 #135600 on…
- PDB
- 5U3V
- Type
- protein
- Length
- 531 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Peroxisome proliferator-activated receptor delta
- UniProt
- Q03181
- Ligands
- B7G, 7TY
- Pockets
- 4 · best druggability 0.87
Structure
x-ray diffraction · 2 distinct chains · 68% helix, 5% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Peroxisome proliferator-activated receptor delta | protein | 263 | 68% helix, 5% strand | Q03181 |
| B | Peroxisome proliferator-activated receptor delta | protein | 268 | 68% helix, 5% strand | Q03181 |
Ligands and binding sites
- B7G · heptyl beta-D-glucopyranoside · ligand · 2 copies · chains A, B
- 7TY · 6-[2-({cyclopentyl[4-(furan-3-yl)benzene-1-carbonyl]amino}methyl)phenoxy]hexanoic acid · ligand · 2 copies · chains A, B
- PEG · Di(hydroxyethyl)ether · additive · 6 copies · chains A, B
- PGO · S-1,2-propanediol · additive · 3 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 509 | 0.87 | 0.92 | 53 | 7TY, PGO |
| 2 | 547 | 0.84 | 0.89 | 54 | PGO, 7TY |
| 3 | 489 | 0.74 | 0.82 | 54 | B7G |
| 4 | 99 | 0.41 | 0.77 | 14 | empty |
Interfaces
1 interface between chains.
- A–B · 746 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 modified (artifact).
Compared structures
- 5U3V · Human PPARdelta ligand-binding domain in complexed with specific agonist 6 · 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 5U3V · PDBe 5U3V · UniProt Q03181
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