Research workbench
Human ppardelta ligand-binding domain in complexed with GW501516
Analyse Human ppardelta ligand-binding domain in complexed with GW501516 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5U46
- Type
- protein
- Length
- 528 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, 7T1
- Pockets
- 7 · best druggability 0.86
Structure
x-ray diffraction · 1 distinct chain · 68% helix, 5% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Peroxisome proliferator-activated receptor delta | protein | 264 | 68% helix, 5% strand | Q03181 |
Ligands and binding sites
- B7G · heptyl beta-D-glucopyranoside · ligand · 2 copies · chains A, B
- 7T1 · {2-methyl-4-[({4-methyl-2-[4-(trifluoromethyl)phenyl]-1,3-thiazol-5-yl}methyl)sulfanyl]phenoxy}acetic acid · ligand · 2 copies · chains A, B
- PGO · S-1,2-propanediol · additive · 2 copies · chains A
- PEG · Di(hydroxyethyl)ether · additive · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 542 | 0.86 | 0.91 | 57 | 7T1 |
| 2 | 644 | 0.85 | 0.89 | 63 | PGO, 7T1 |
| 3 | 462 | 0.75 | 0.83 | 53 | B7G |
| 4 | 106 | 0.45 | 0.79 | 18 | empty |
| 5 | 117 | 0.44 | 0.77 | 18 | empty |
Interfaces
1 interface between chains.
- A–B · 650 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 5U46 · Human PPARdelta ligand-binding domain in complexed with GW501516 · 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 5U46 · PDBe 5U46 · UniProt Q03181
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