MolNFT v1 · #152507 · protein
Human ppargamma ligand binding domain complexed with SB1494
6IJS · Peroxisome proliferator-activated receptor gamma: “Human ppargamma ligand binding domain complexed with SB1494”. X-ray diffraction, 1 ligand (A9F), 2 pockets (best druggability 0.85). MolNFT v1 #152507 on GenesisL1: 3D structure…
- PDB
- 6IJS
- Type
- protein
- Length
- 274 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Peroxisome proliferator-activated receptor gamma; 16-mer peptide from nuclear receptor…
- EC
- 2.3.1.48
- UniProt
- P37231, Q15788
- Ligands
- A9F
- Pockets
- 2 · best druggability 0.85
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 | 263 | 67% helix, 5% strand | P37231 |
| B | 16-mer peptide from nuclear receptor coactivator 1 (EC 2.3.1.48) | protein | 11 | 73% helix, 0% strand | Q15788 |
Ligands and binding sites
- A9F · N-{[3-({[(1R,2S)-2-{[(2E)-2-cyano-4,4-dimethylpent-2-enoyl]amino}cyclopentyl]oxy}methyl)phenyl]methyl}-4-[(4-methylpiperazin-1-yl)methyl]benzamide · 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 | 613 | 0.85 | 0.89 | 55 | A9F |
| 2 | 55 | 0.40 | 0.81 | 15 | empty |
Interfaces
1 interface between chains.
- A–B · 627 Ų buried · 8 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 covalent (covalent ligand).
Compared structures
- 6IJS · Human PPARgamma ligand binding domain complexed with SB1494 · 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
- Every structure of UniProt Q15788
- Elsewhere: RCSB PDB 6IJS · PDBe 6IJS · UniProt P37231 · UniProt Q15788
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