MolNFT v1 · #164788 · protein
Crystal structure of the complex between ppargamma lbd and the ligand NV1346 (3A)
6T9C · Peroxisome proliferator-activated receptor gamma: “Crystal structure of the complex between ppargamma lbd and the ligand NV1346 (3A)”. X-ray diffraction, 1 ligand (MX8), 9 pockets (best druggability 0.78). MolNFT v1 #164788 on…
- PDB
- 6T9C
- Type
- protein
- Length
- 499 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Peroxisome proliferator-activated receptor gamma
- UniProt
- P37231
- Ligands
- MX8
- Pockets
- 9 · best druggability 0.78
Structure
x-ray diffraction · 2 distinct chains · 66% helix, 5% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Peroxisome proliferator-activated receptor gamma | protein | 251 | 68% helix, 5% strand | P37231 |
| B | Peroxisome proliferator-activated receptor gamma | protein | 248 | 65% helix, 5% strand | P37231 |
Ligands and binding sites
- MX8 · 4-hexoxy-~{N}-[(2~{S})-3-methyl-1-(oxidanylamino)-1-oxidanylidene-butan-2-yl]benzamide · ligand · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 470 | 0.78 | 0.85 | 51 | MX8 |
| 2 | 525 | 0.78 | 0.84 | 57 | empty |
| 3 | 106 | 0.61 | 0.87 | 21 | empty |
| 4 | 292 | 0.59 | 0.78 | 26 | empty |
| 5 | 212 | 0.53 | 0.77 | 21 | empty |
Interfaces
1 interface between chains.
- A–B · 1132 Ų buried · 13 hydrogen bonds · protein-protein
Compared structures
- 6T9C · Crystal structure of the complex between PPARgamma LBD and the ligand NV1346 (3a) · the same entry in another collection · chain A against A, TM-score 1.00
- P37231 · AlphaFold monomer V2.0 prediction for peroxisome proliferator- activated receptor gamma… · a predicted model of the same protein · chain A against A, TM-score 0.99
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 6T9C · PDBe 6T9C · UniProt P37231
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