MolNFT v1 · #135603 · protein
Human ppardelta ligand-binding domain in complexed with specific agonist 9
5U3Y · Peroxisome proliferator-activated receptor delta: “Human ppardelta ligand-binding domain in complexed with specific agonist 9”. X-ray diffraction, 2 ligands (B7G, 7U7), 5 pockets (best druggability 0.83). MolNFT v1 #135603 on…
- PDB
- 5U3Y
- Type
- protein
- Length
- 518 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, 7U7
- Pockets
- 5 · best druggability 0.83
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 | 263 | 66% helix, 5% strand | Q03181 |
| B | Peroxisome proliferator-activated receptor delta | protein | 255 | 68% helix, 5% strand | Q03181 |
Ligands and binding sites
- B7G · heptyl beta-D-glucopyranoside · ligand · 2 copies · chains A, B
- 7U7 · 6-[2-({cyclopropyl[4-(furan-2-yl)benzene-1-carbonyl]amino}methyl)phenoxy]hexanoic acid · ligand · 2 copies · chains A, B
- PEG · Di(hydroxyethyl)ether · additive · 6 copies · chains A, B
- PGO · S-1,2-propanediol · additive · 3 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, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 504 | 0.83 | 0.89 | 51 | 7U7, PGO |
| 2 | 512 | 0.83 | 0.89 | 53 | 7U7, PEG |
| 3 | 446 | 0.74 | 0.83 | 47 | B7G, PEG |
| 4 | 212 | 0.54 | 0.78 | 30 | PGO |
| 5 | 191 | 0.53 | 0.78 | 30 | empty |
Interfaces
1 interface between chains.
- A–B · 660 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 5U3Y · Human PPARdelta ligand-binding domain in complexed with specific agonist 9 · 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 5U3Y · PDBe 5U3Y · UniProt Q03181
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