Research workbench
Crystal structure of ppargamma ligand binding domain in complex with dibenzooxepine derivative compound-17
Analyse Crystal structure of ppargamma ligand binding domain in complex with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6K0T
- Type
- protein
- Length
- 551 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Peroxisome proliferator-activated receptor gamma; Peroxisome proliferator-activated…
- UniProt
- P37231
- Ligands
- CTU
- Pockets
- 9 · best druggability 0.85
Structure
x-ray diffraction · 4 distinct chains · 65% helix, 5% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Peroxisome proliferator-activated receptor gamma | protein | 261 | 66% helix, 5% strand | P37231 |
| B | Peroxisome proliferator-activated receptor gamma coactivator 1-alpha | protein | 10 | 60% helix, 0% strand | — |
| C | Peroxisome proliferator-activated receptor gamma | protein | 268 | 65% helix, 5% strand | P37231 |
| D | Peroxisome proliferator-activated receptor gamma coactivator 1-alpha | protein | 12 | 58% helix, 0% strand | — |
Ligands and binding sites
- CTU · 3-[(1~{E})-1-[8-[(8-chloranyl-2-cyclopropyl-imidazo[1, 2-a]pyridin-3-yl)methyl]-3-fluoranyl-6~{H}-benzo[c][1]benzoxepin-11-ylidene]ethyl]-4~{H}-1,2,4-oxadiazol-5-one · ligand · 2 copies · chains A, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 385 | 0.85 | 0.93 | 46 | CTU |
| 2 | 433 | 0.82 | 0.90 | 51 | CTU |
| 3 | 544 | 0.71 | 0.80 | 50 | empty |
| 4 | 61 | 0.42 | 0.81 | 10 | empty |
| 5 | 157 | 0.42 | 0.74 | 22 | empty |
Interfaces
3 interfaces between chains.
- C–D · 554 Ų buried · 8 hydrogen bonds · protein-protein
- A–B · 529 Ų buried · 8 hydrogen bonds · protein-protein
- A–C · 306 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 modified (artifact).
Compared structures
- 6K0T · 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
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 6K0T · PDBe 6K0T · UniProt P37231
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