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Crystal structure of the complex between ppargamma-lbd and the R enantiomer of mbx-102 (metaglidasen)
Analyse Crystal structure of the complex between ppargamma-lbd and the R enantiomer of… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4PVU
- Type
- protein
- Length
- 509 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Peroxisome proliferator-activated receptor gamma
- UniProt
- P37231
- Ligands
- MGZ
- Pockets
- 6 · best druggability 0.77
Structure
x-ray diffraction · 2 distinct chains · 66% helix, 6% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Peroxisome proliferator-activated receptor gamma | protein | 257 | 65% helix, 6% strand | P37231 |
| B | Peroxisome proliferator-activated receptor gamma | protein | 252 | 66% helix, 5% strand | P37231 |
Ligands and binding sites
- MGZ · (2R)-(4-chlorophenyl)[3-(trifluoromethyl)phenoxy]ethanoic acid · ligand · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 395 | 0.77 | 0.86 | 44 | empty |
| 2 | 575 | 0.76 | 0.82 | 68 | MGZ |
| 3 | 153 | 0.62 | 0.85 | 24 | empty |
| 4 | 223 | 0.58 | 0.80 | 26 | empty |
| 5 | 116 | 0.52 | 0.82 | 27 | empty |
Interfaces
1 interface between chains.
- A–B · 1050 Ų buried · 19 hydrogen bonds · protein-protein
Compared structures
- 4PVU · Crystal structure of the complex between PPARgamma-LBD and the R enantiomer of Mbx-102… · 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 4PVU · PDBe 4PVU · UniProt P37231
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