MolNFT v1 · #138680 · protein
Covalent bond formation of synthetic ligand with hpparg-lbd
5WQX · Peroxisome proliferator-activated receptor gamma: “Covalent bond formation of synthetic ligand with hpparg-lbd”. X-ray diffraction, 1 ligand (T65), 6 pockets (best druggability 0.77). MolNFT v1 #138680 on GenesisL1: 3D structure…
- PDB
- 5WQX
- Type
- protein
- Length
- 503 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Peroxisome proliferator-activated receptor gamma
- UniProt
- P37231
- Ligands
- T65
- Pockets
- 6 · best druggability 0.77
Structure
x-ray diffraction · 2 distinct chains · 68% helix, 5% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Peroxisome proliferator-activated receptor gamma | protein | 257 | 66% helix, 5% strand | P37231 |
| B | Peroxisome proliferator-activated receptor gamma | protein | 246 | 71% helix, 5% strand | P37231 |
Ligands and binding sites
- T65 · 2-[E-(E-2-oxidanylidenehexadec-5-enylidene) amino]ethanoic acid · ligand · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 527 | 0.77 | 0.84 | 57 | T65 |
| 2 | 870 | 0.77 | 0.80 | 88 | empty |
| 3 | 313 | 0.61 | 0.79 | 24 | empty |
| 4 | 120 | 0.52 | 0.82 | 27 | empty |
| 5 | 98 | 0.47 | 0.80 | 17 | empty |
Interfaces
1 interface between chains.
- A–B · 977 Ų buried · 13 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 covalent (covalent ligand).
Compared structures
- 5WQX · Covalent bond formation of synthetic ligand with hPPARg-LBD · 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 5WQX · PDBe 5WQX · UniProt P37231
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