Research workbench
Crystal structure of the complex between ppargamma and the partial agonist LT127 (ureidofibrate derivative). this structure has been obtained from crystals soaked for 6 hours.
Analyse Crystal structure of the complex between ppargamma and the partial agonist… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2I4Z
- Type
- protein
- Length
- 540 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Peroxisome proliferator-activated receptor gamma
- UniProt
- P37231
- Ligands
- DRH
- Pockets
- 11 · best druggability 0.86
Structure
x-ray diffraction · 1 distinct chain · 66% helix, 5% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Peroxisome proliferator-activated receptor gamma | protein | 270 | 66% helix, 5% strand | P37231 |
Ligands and binding sites
- DRH · (2S)-2-(4-{2-[1,3-benzoxazol-2-yl(heptyl)amino]ethyl}phenoxy)-2-methylbutanoic acid · ligand · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 508 | 0.86 | 0.92 | 60 | empty |
| 2 | 580 | 0.83 | 0.88 | 58 | DRH |
| 3 | 207 | 0.68 | 0.86 | 23 | empty |
| 4 | 185 | 0.60 | 0.82 | 23 | empty |
| 5 | 124 | 0.53 | 0.82 | 27 | empty |
Interfaces
1 interface between chains.
- A–B · 1049 Ų buried · 14 hydrogen bonds · protein-protein
Compared structures
- 2I4Z · Crystal structure of the complex between PPARgamma and the partial agonist LT127… · 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 P37231
- Elsewhere: RCSB PDB 2I4Z · PDBe 2I4Z · UniProt P37231
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