Research workbench
Crystal structure of PPARG and NCOR2 with an inverse agonist (compound 15b)
Analyse Crystal structure of PPARG and NCOR2 with an inverse agonist (compound 15b) in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 8B93
- Type
- protein
- Length
- 513 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 2.21
- Source
- Homo sapiens; SYNTHETIC CONSTRUCT
- Molecule
- Peroxisome proliferator-activated receptor gamma; Nuclear receptor corepressor 2
- UniProt
- P37231, Q9Y618
- Ligands
- Q8F
- Pockets
- 5 · best druggability 0.80
Structure
x-ray diffraction · resolution 2.21 · 4 distinct chains · 67% helix, 5% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Peroxisome proliferator-activated receptor gamma | protein | 248 | 66% helix, 5% strand | P37231 |
| B | Peroxisome proliferator-activated receptor gamma | protein | 241 | 67% helix, 5% strand | P37231 |
| C | Nuclear receptor corepressor 2 | protein | 12 | 83% helix, 0% strand | Q9Y618 |
| D | Nuclear receptor corepressor 2 | protein | 12 | 83% helix, 0% strand | Q9Y618 |
Ligands and binding sites
- Q8F · 4-chloranyl-6-fluoranyl-~{N}1-[[4-fluoranyl-2-(2-methoxyethoxymethyl)phenyl]methyl]-~{N}3-[2-methyl-4-(trifluoromethyl)phenyl]benzene-1,3-dicarboxamide · ligand · 2 copies · chains A, C, B, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 908 | 0.80 | 0.82 | 110 | Q8F |
| 2 | 495 | 0.76 | 0.84 | 63 | Q8F |
| 3 | 260 | 0.52 | 0.75 | 29 | empty |
| 4 | 120 | 0.48 | 0.80 | 23 | empty |
| 5 | 60 | 0.29 | 0.74 | 12 | empty |
Interfaces
3 interfaces between chains.
- A–B · 869 Ų buried · 13 hydrogen bonds · protein-protein
- B–D · 547 Ų buried · 1 hydrogen bond · protein-protein
- A–C · 500 Ų buried · 3 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 covalent (covalent ligand).
Compared structures
- Q9Y618 · AlphaFold monomer V2.0 prediction for nuclear receptor corepressor 2 (Q9Y618) · a predicted model of the same protein · chain C against A, TM-score 0.82
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 Q9Y618
- Elsewhere: RCSB PDB 8B93 · PDBe 8B93 · UniProt P37231 · UniProt Q9Y618
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