MolNFT v1 · #146415 · protein
Crystal structure of human ppargamma ligand binding domain in complex with CAY10638
6DGR · Peroxisome proliferator-activated receptor gamma: “Crystal structure of human ppargamma ligand binding domain in complex with CAY10638”. X-ray diffraction, 1 ligand (GDY), 8 pockets (best druggability 0.82). MolNFT v1 #146415 on…
- PDB
- 6DGR
- Type
- protein
- Length
- 515 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Peroxisome proliferator-activated receptor gamma
- UniProt
- P37231
- Ligands
- GDY
- Pockets
- 8 · best druggability 0.82
Structure
x-ray diffraction · 2 distinct chains · 67% helix, 5% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Peroxisome proliferator-activated receptor gamma | protein | 261 | 68% helix, 5% strand | P37231 |
| B | Peroxisome proliferator-activated receptor gamma | protein | 254 | 65% helix, 5% strand | P37231 |
Ligands and binding sites
- GDY · (5Z)-5-({4-[2-(thiophen-2-yl) ethoxy]phenyl}methylidene)-1,3-thiazolidine-2,4-dione · ligand · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 426 | 0.82 | 0.89 | 47 | GDY |
| 2 | 561 | 0.81 | 0.87 | 58 | empty |
| 3 | 320 | 0.65 | 0.80 | 38 | empty |
| 4 | 202 | 0.64 | 0.83 | 23 | empty |
| 5 | 101 | 0.61 | 0.88 | 21 | empty |
Interfaces
1 interface between chains.
- A–B · 1070 Ų buried · 15 hydrogen bonds · protein-protein
Compared structures
- 6DGR · Crystal Structure of Human PPARgamma Ligand Binding Domain in Complex with CAY10638 · 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 6DGR · PDBe 6DGR · UniProt P37231
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