MolNFT v1 · #145963 · protein
Pparg lbd in complex with SR1988
6D3E · Peroxisome proliferator-activated receptor gamma: “Pparg lbd in complex with SR1988”. X-ray diffraction, 1 ligand (FT7), 9 pockets (best druggability 0.84). MolNFT v1 #145963 on GenesisL1: 3D structure, binding sites and pockets in…
- PDB
- 6D3E
- Type
- protein
- Length
- 526 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Peroxisome proliferator-activated receptor gamma
- UniProt
- P37231
- Ligands
- FT7
- Pockets
- 9 · best druggability 0.84
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 | 263 | 66% helix, 5% strand | P37231 |
| B | Peroxisome proliferator-activated receptor gamma | protein | 263 | 63% helix, 5% strand | P37231 |
Ligands and binding sites
- FT7 · 1-[(2,4-difluorophenyl)methyl]-2,3-dimethyl-N-[(1R)-1-phenylpropyl]-1H-indole-5-carboxamide · 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, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 393 | 0.84 | 0.92 | 49 | empty |
| 2 | 572 | 0.79 | 0.85 | 58 | FT7 |
| 3 | 189 | 0.63 | 0.83 | 17 | empty |
| 4 | 287 | 0.60 | 0.79 | 23 | empty |
| 5 | 121 | 0.60 | 0.86 | 23 | empty |
Interfaces
1 interface between chains.
- A–B · 961 Ų buried · 6 hydrogen bonds · protein-protein
Compared structures
- 6D3E · PPARg LBD in Complex with SR1988 · 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 6D3E · PDBe 6D3E · UniProt P37231
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