Research workbench
Ppardelta complexed with an anthranilic acid partial agonist
Analyse Ppardelta complexed with an anthranilic acid partial agonist in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3DY6
- Type
- protein
- Length
- 512 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Peroxisome proliferator-activated receptor delta
- UniProt
- Q03181
- Ligands
- DY6, 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 | 257 | 70% helix, 5% strand | Q03181 |
| B | Peroxisome proliferator-activated receptor delta | protein | 255 | 69% helix, 5% strand | Q03181 |
Ligands and binding sites
- DY6 · 2-({[3-(3,4-dihydroisoquinolin-2(1H)-ylsulfonyl)phenyl]carbonyl}amino)benzoic acid · ligand · 2 copies · chains A, B
- IOD · Iodide ion · ion · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 456 | 0.83 | 0.89 | 46 | DY6 |
| 2 | 454 | 0.83 | 0.89 | 48 | DY6 |
| 3 | 76 | 0.43 | 0.80 | 13 | empty |
| 4 | 86 | 0.39 | 0.77 | 14 | empty |
| 5 | 50 | 0.28 | 0.74 | 9 | empty |
Interfaces
1 interface between chains.
- A–B · 19 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 3DY6 · PPARdelta complexed with an anthranilic acid partial agonist · 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 3DY6 · PDBe 3DY6 · UniProt Q03181
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