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Crystal structure of human ppargamma ligand binding domain in complex with edaglitazone
Analyse Crystal structure of human ppargamma ligand binding domain in complex with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5UGM
- 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
- P37231
- Ligands
- 8A7, KNA
- Pockets
- 11 · best druggability 0.84
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 | 271 | 66% helix, 5% strand | P37231 |
Ligands and binding sites
- 8A7 · (5R)-5-({4-[2-(5-methyl-2-phenyl-1,3-oxazol-4-yl) ethoxy]-1-benzothiophen-7-yl}methyl)-1,3-thiazolidine-2,4-dione · ligand · 4 copies · chains A, B
- KNA · nonanoic acid · ligand · 2 copies · chains A, B
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 | 528 | 0.84 | 0.90 | 65 | 8A7, KNA |
| 2 | 519 | 0.84 | 0.90 | 64 | 8A7, KNA |
| 3 | 123 | 0.60 | 0.85 | 20 | empty |
| 4 | 87 | 0.59 | 0.88 | 18 | empty |
| 5 | 225 | 0.56 | 0.78 | 29 | empty |
Interfaces
1 interface between chains.
- A–B · 1179 Ų buried · 21 hydrogen bonds · protein-protein
Compared structures
- 5UGM · Crystal Structure of Human PPARgamma Ligand Binding Domain in Complex with Edaglitazone · 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 5UGM · PDBe 5UGM · UniProt P37231
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