MolNFT v1 · #189800 · protein
Human peroxisome proliferator-activated receptor (ppar) delta ligand binding domain in complex with a synthetic agonist JKPL39
7VWH · Peroxisome proliferator-activated receptor delta: “Human peroxisome proliferator-activated receptor (ppar) delta ligand binding domain in complex with a…”. X-ray diffraction, 2 ligands (82K, B7G), 7 pockets (best druggability 0.83).…
- PDB
- 7VWH
- 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
- 82K, B7G
- Pockets
- 7 · 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 | 258 | 67% helix, 5% strand | Q03181 |
| B | Peroxisome proliferator-activated receptor delta | protein | 258 | 67% helix, 5% strand | Q03181 |
Ligands and binding sites
- 82K · (2S)-2-[[4-hexoxy-3-[[[4-(trifluoromethyl) phenyl]carbonylamino]methyl]phenyl]methyl]butanoic acid · ligand · 2 copies · chains A, B
- B7G · heptyl beta-D-glucopyranoside · ligand · 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 | 481 | 0.83 | 0.89 | 48 | 82K |
| 2 | 519 | 0.82 | 0.88 | 52 | 82K |
| 3 | 444 | 0.73 | 0.82 | 47 | B7G |
| 4 | 115 | 0.43 | 0.77 | 17 | empty |
| 5 | 90 | 0.41 | 0.78 | 12 | empty |
Interfaces
1 interface between chains.
- A–B · 678 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 7VWH · human peroxisome proliferator-activated receptor (PPAR) delta ligand binding domain in… · 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 7VWH · PDBe 7VWH · UniProt Q03181
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