Research workbench
Crystal structure of peroxisome proliferator-activated receptor delta (PPARD)LBD in complex with DN003316
Analyse Crystal structure of peroxisome proliferator-activated receptor delta… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6A6P
- Type
- protein
- Length
- 533 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Peroxisome proliferator-activated receptor delta
- UniProt
- Q03181
- Ligands
- 9RF, B7G
- Pockets
- 3 · best druggability 0.84
Structure
x-ray diffraction · 2 distinct chains · 66% helix, 5% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Peroxisome proliferator-activated receptor delta | protein | 266 | 67% helix, 5% strand | Q03181 |
| B | Peroxisome proliferator-activated receptor delta | protein | 267 | 66% helix, 5% strand | Q03181 |
Ligands and binding sites
- 9RF · {2-methyl-4-[({5-[4-(trifluoromethyl)phenyl]-1,3,4-thiadiazol-2-yl}methyl)sulfanyl]phenoxy}acetic acid · ligand · 2 copies · chains A, B
- B7G · heptyl beta-D-glucopyranoside · ligand · 2 copies · chains A, B
- PE3 · 3,6,9,12,15,18,21,24,27,30,33,36,39-tridecaoxahentetracontane-1,41-diol · additive · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 541 | 0.84 | 0.89 | 60 | 9RF, B7G |
| 2 | 531 | 0.83 | 0.89 | 63 | 9RF, B7G |
| 3 | 648 | 0.76 | 0.82 | 58 | PE3 |
Interfaces
1 interface between chains.
- A–B · 546 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 covalent (additive adduct).
Compared structures
- 6A6P · Crystal Structure of Peroxisome Proliferator-Activated Receptor Delta (PPARd)LBD 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 6A6P · PDBe 6A6P · UniProt Q03181
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