Research workbench
Structure-based drug design of a novel family of ppar partial agonists: virtual screening, X-ray crystallography and in VITRO/IN vivo biological activities
Analyse Structure-based drug design of a novel family of ppar partial agonists: virtual… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2G0H
- Type
- protein
- Length
- 542 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Peroxisome proliferator-activated receptor gamma
- UniProt
- Q86U60
- Ligands
- SP3
- Pockets
- 5 · best druggability 0.85
Structure
x-ray diffraction · 1 distinct chain · 62% helix, 2% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Peroxisome proliferator-activated receptor gamma | protein | 271 | 62% helix, 2% strand | Q86U60 |
Ligands and binding sites
- SP3 · N-[1-(4-fluorophenyl)-3-(2-thienyl)-1H-pyrazol-5-yl]-3,5-bis(trifluoromethyl)benzenesulfonamide · ligand · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 787 | 0.85 | 0.88 | 81 | SP3 |
| 2 | 713 | 0.84 | 0.87 | 75 | SP3 |
| 3 | 682 | 0.77 | 0.82 | 68 | empty |
| 4 | 146 | 0.42 | 0.75 | 24 | empty |
| 5 | 65 | 0.29 | 0.74 | 14 | empty |
Interfaces
1 interface between chains.
- A–B · 793 Ų buried · 9 hydrogen bonds · protein-protein
Compared structures
- 2G0H · Structure-based drug design of a novel family of PPAR partial agonists: virtual… · 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 Q86U60
- Elsewhere: RCSB PDB 2G0H · PDBe 2G0H · UniProt Q86U60
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