Research workbench
Huisgen cycloaddition for pparg-lbd labeling by soaking method
Analyse Huisgen cycloaddition for pparg-lbd labeling by soaking method in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5WR0
- Type
- protein
- Length
- 503 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Peroxisome proliferator-activated receptor gamma
- UniProt
- P37231
- Ligands
- 8Y0
- Pockets
- 7 · best druggability 0.77
Structure
x-ray diffraction · 2 distinct chains · 70% helix, 5% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Peroxisome proliferator-activated receptor gamma | protein | 257 | 70% helix, 5% strand | P37231 |
| B | Peroxisome proliferator-activated receptor gamma | protein | 246 | 70% helix, 5% strand | P37231 |
Ligands and binding sites
- 8Y0 · (E)-N-[(3E)-2-oxo-16-(8-{6-[(trifluoroacetyl) amino]hexanoyl}-8,9-dihydro-1H-dibenzo[b,f][1,2, 3]triazolo[4,5-d]azocin-1-yl)hexadec-3-en-1-ylidene]glycine · ligand · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 469 | 0.77 | 0.85 | 51 | 8Y0 |
| 2 | 536 | 0.77 | 0.84 | 61 | empty |
| 3 | 681 | 0.71 | 0.78 | 62 | empty |
| 4 | 145 | 0.44 | 0.76 | 22 | empty |
| 5 | 120 | 0.39 | 0.74 | 16 | empty |
Interfaces
1 interface between chains.
- A–B · 948 Ų buried · 9 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 covalent (covalent ligand).
Compared structures
- 5WR0 · Huisgen cycloaddition for PPARg-LBD labeling by soaking method · 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 5WR0 · PDBe 5WR0 · UniProt P37231
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