MolNFT v1 · #135595 · protein
Human ppardelta ligand-binding domain in complexed with specific agonist 1
5U3Q · Peroxisome proliferator-activated receptor delta: “Human ppardelta ligand-binding domain in complexed with specific agonist 1”. X-ray diffraction, 4 ligands (7UJ, B7G, K), 5 pockets (best druggability 0.87). MolNFT v1 #135595 on…
- PDB
- 5U3Q
- Type
- protein
- Length
- 536 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Peroxisome proliferator-activated receptor delta
- UniProt
- Q03181
- Ligands
- 7UJ, B7G, K, CL
- Pockets
- 5 · 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 | 265 | 68% helix, 5% strand | Q03181 |
| B | Peroxisome proliferator-activated receptor delta | protein | 271 | 68% helix, 5% strand | Q03181 |
Ligands and binding sites
- 7UJ · 6-(2-{[([1,1'-biphenyl]-4-carbonyl)(propan-2-yl) amino]methyl}phenoxy)hexanoic acid · ligand · 2 copies · chains A, B
- B7G · heptyl beta-D-glucopyranoside · ligand · 2 copies · chains A, B
- K · Potassium ion · metal · 2 copies · chains A, B
- CL · Chloride ion · ion · 2 copies · chains B
- PGO · S-1,2-propanediol · additive · 8 copies · chains A, B
- PEG · Di(hydroxyethyl)ether · additive · 7 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 | 552 | 0.87 | 0.92 | 58 | 7UJ, PGO |
| 2 | 639 | 0.86 | 0.90 | 63 | 7UJ, PGO |
| 3 | 445 | 0.73 | 0.82 | 41 | B7G |
| 4 | 102 | 0.42 | 0.77 | 16 | empty |
| 5 | 54 | 0.25 | 0.73 | 14 | empty |
Interfaces
1 interface between chains.
- A–B · 752 Ų buried · 1 hydrogen bond · protein-protein
Compared structures
- 5U3Q · Human PPARdelta ligand-binding domain in complexed with specific agonist 1 · 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 5U3Q · PDBe 5U3Q · UniProt Q03181
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