Research workbench
Human ppardelta ligand-binding domain in complexed with specific agonist 15
Analyse Human ppardelta ligand-binding domain in complexed with specific agonist 15 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5U40
- Type
- protein
- Length
- 516 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Peroxisome proliferator-activated receptor delta
- UniProt
- Q03181
- Ligands
- 7UD, B7G
- Pockets
- 6 · best druggability 0.85
Structure
x-ray diffraction · 2 distinct chains · 69% helix, 5% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Peroxisome proliferator-activated receptor delta | protein | 257 | 69% helix, 5% strand | Q03181 |
| B | Peroxisome proliferator-activated receptor delta | protein | 259 | 68% helix, 5% strand | Q03181 |
Ligands and binding sites
- 7UD · 6-[2-({benzyl[4-(furan-3-yl)benzene-1-carbonyl]amino}methyl)phenoxy]hexanoic acid · ligand · 2 copies · chains A, B
- B7G · heptyl beta-D-glucopyranoside · ligand · 2 copies · chains A, B
- PGO · S-1,2-propanediol · additive · 5 copies · chains A, B
- PEG · Di(hydroxyethyl)ether · additive · 4 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 508 | 0.85 | 0.91 | 57 | 7UD, PGO |
| 2 | 590 | 0.83 | 0.88 | 66 | 7UD, PEG |
| 3 | 475 | 0.73 | 0.82 | 51 | B7G |
| 4 | 80 | 0.38 | 0.77 | 16 | empty |
| 5 | 81 | 0.37 | 0.77 | 13 | PGO |
Interfaces
1 interface between chains.
- A–B · 666 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 5U40 · Human PPARdelta ligand-binding domain in complexed with specific agonist 15 · 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 5U40 · PDBe 5U40 · UniProt Q03181
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