Research workbench
Human ppargamma ligand-binding domain R288A mutant in complex with imatinib
Analyse Human ppargamma ligand-binding domain R288A mutant in complex with imatinib in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6KTN
- Type
- protein
- Length
- 275 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
- STI
- Pockets
- 2 · best druggability 0.84
Structure
x-ray diffraction · 2 distinct chains · 66% helix, 4% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Peroxisome proliferator-activated receptor gamma | protein | 264 | 66% 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
- STI · 4-(4-methyl-piperazin-1-ylmethyl)-N-[4-methyl-3-(4-pyridin-3-yl-pyrimidin-2-ylamino)-phenyl]-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 | 519 | 0.84 | 0.90 | 55 | STI |
| 2 | 51 | 0.30 | 0.76 | 12 | empty |
Interfaces
1 interface between chains.
- A–B · 639 Ų buried · 10 hydrogen bonds · protein-protein
Compared structures
- 6KTN · Human PPARgamma ligand-binding domain R288A mutant in complex with imatinib · 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 6KTN · PDBe 6KTN · UniProt P37231 · UniProt Q15788
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