MolNFT v1 · #142718 · protein
Crystal structure of ppargamma ligand binding domain in complex with dibenzooxepine derivative compound-9
6AD9 · Peroxisome proliferator-activated receptor gamma: “Crystal structure of ppargamma ligand binding domain in complex with dibenzooxepine derivative compound-9”. X-ray diffraction, 1 ligand (KK4), 2 pockets (best druggability 0.83).…
- PDB
- 6AD9
- Type
- protein
- Length
- 265 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Peroxisome proliferator-activated receptor gamma; 12-mer peptide from peroxisome…
- UniProt
- P37231, Q9UBK2
- Ligands
- KK4
- Pockets
- 2 · best druggability 0.83
Structure
x-ray diffraction · 2 distinct chains · 65% helix, 5% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Peroxisome proliferator-activated receptor gamma | protein | 255 | 65% helix, 5% strand | P37231 |
| B | 12-mer peptide from peroxisome proliferator-activated receptor gamma coactivator 1-alpha | protein | 10 | 70% helix, 0% strand | Q9UBK2 |
Ligands and binding sites
- KK4 · 3-[(1E)-1-{8-[(4-methyl-2-propyl-1H-benzimidazol-1-yl) methyl]dibenzo[b,e]oxepin-11(6H)-ylidene}ethyl]-1,2,4-oxadiazol-5(4H)-one · ligand · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 568 | 0.83 | 0.88 | 60 | KK4 |
| 2 | 72 | 0.38 | 0.78 | 16 | empty |
Interfaces
1 interface between chains.
- A–B · 517 Ų buried · 8 hydrogen bonds · protein-protein
Compared structures
- 6AD9 · Crystal Structure of PPARgamma Ligand Binding Domain in complex with dibenzooxepine… · the same entry in another collection · chain A against A, TM-score 1.00
- Q9UBK2 · AlphaFold monomer V2.0 prediction for peroxisome proliferator- activated receptor gamma… · a predicted model of the same protein · chain B against A, TM-score 0.84
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
- Every structure of UniProt Q9UBK2
- Elsewhere: RCSB PDB 6AD9 · PDBe 6AD9 · UniProt P37231 · UniProt Q9UBK2
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