Research workbench
Human ppardelta ligand-binding domain in complexed with specific agonist 4
Analyse Human ppardelta ligand-binding domain in complexed with specific agonist 4 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5U3T
- Type
- protein
- Length
- 537 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Peroxisome proliferator-activated receptor delta
- UniProt
- Q03181
- Ligands
- 7UY, B7G
- Pockets
- 6 · best druggability 0.87
Structure
x-ray diffraction · 2 distinct chains · 67% helix, 5% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Peroxisome proliferator-activated receptor delta | protein | 271 | 68% helix, 5% strand | Q03181 |
| B | Peroxisome proliferator-activated receptor delta | protein | 266 | 67% helix, 5% strand | Q03181 |
Ligands and binding sites
- 7UY · 6-[2-({(propan-2-yl)[4-(thiophen-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 · 9 copies · chains A, B
- PEG · Di(hydroxyethyl)ether · additive · 6 copies · chains A, B
- PGE · Triethylene glycol · additive · chains 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 | 491 | 0.87 | 0.93 | 51 | 7UY, PGO, PEG |
| 2 | 518 | 0.86 | 0.91 | 54 | 7UY, PGO |
| 3 | 472 | 0.75 | 0.83 | 54 | B7G |
| 4 | 98 | 0.41 | 0.77 | 15 | empty |
| 5 | 59 | 0.40 | 0.80 | 13 | PEG |
Interfaces
1 interface between chains.
- A–B · 733 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 modified (artifact).
Compared structures
- 5U3T · Human PPARdelta ligand-binding domain in complexed with specific agonist 4 · 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 5U3T · PDBe 5U3T · UniProt Q03181
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