Research workbench
Structure of ppargamma ligand binding domain in complex with (R)-5-(3- ((3-(6-METHOXYBENZO[D]ISOXAZOL-3-yl)-2-oxo-2,3-dihydro-1H- BENZO[D]IMIDAZOL-1-YL)METHYL)PHENYL)-5-methyloxazolidine-2,4-dione
Analyse Structure of ppargamma ligand binding domain in complex with (R)-5-(3… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3TY0
- Type
- protein
- Length
- 554 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Peroxisome proliferator-activated receptor gamma
- UniProt
- P37231
- Ligands
- 082
- Pockets
- 10 · best druggability 0.84
Structure
x-ray diffraction · 1 distinct chain · 65% helix, 5% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Peroxisome proliferator-activated receptor gamma | protein | 277 | 65% helix, 5% strand | P37231 |
Ligands and binding sites
- 082 · (5R)-5-(3-{[3-(6-methoxy-1,2-benzoxazol-3-yl)-2-oxo-2,3-dihydro-1H-benzimidazol-1-yl]methyl}phenyl)-5-methyl-1,3-oxazolidine-2,4-dione · ligand · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 375 | 0.84 | 0.92 | 47 | 082 |
| 2 | 362 | 0.82 | 0.91 | 41 | 082 |
| 3 | 245 | 0.57 | 0.79 | 26 | empty |
| 4 | 93 | 0.56 | 0.86 | 22 | empty |
| 5 | 105 | 0.55 | 0.84 | 19 | empty |
Interfaces
1 interface between chains.
- A–B · 1056 Ų buried · 11 hydrogen bonds · protein-protein
Compared structures
- 3TY0 · Structure of PPARgamma ligand binding domain in complex with… · 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 3TY0 · PDBe 3TY0 · UniProt P37231
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