MolNFT v1 · #142227 · protein
Co-crystal structure of an inhibitor in complex with human ppardelta lbd
5ZXI · Peroxisome proliferator-activated receptor delta: “Co-crystal structure of an inhibitor in complex with human ppardelta lbd”. X-ray diffraction, 1 ligand (9LU), 9 pockets (best druggability 0.83). MolNFT v1 #142227 on GenesisL1: 3D…
- PDB
- 5ZXI
- Type
- protein
- Length
- 496 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Peroxisome proliferator-activated receptor delta
- UniProt
- Q03181
- Ligands
- 9LU
- Pockets
- 9 · best druggability 0.83
Structure
x-ray diffraction · 2 distinct chains · 70% helix, 5% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Peroxisome proliferator-activated receptor delta | protein | 253 | 71% helix, 5% strand | Q03181 |
| B | Peroxisome proliferator-activated receptor delta | protein | 243 | 70% helix, 5% strand | Q03181 |
Ligands and binding sites
- 9LU · 6-[2-({2-[4-(furan-2-yl)phenyl]-5-methyl-1H-imidazol-1-yl}methyl)phenoxy]hexanoic acid · ligand · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 500 | 0.83 | 0.89 | 53 | 9LU |
| 2 | 495 | 0.81 | 0.87 | 53 | 9LU |
| 3 | 98 | 0.43 | 0.78 | 18 | empty |
| 4 | 105 | 0.40 | 0.76 | 17 | empty |
| 5 | 51 | 0.37 | 0.80 | 12 | empty |
Interfaces
1 interface between chains.
- A–B · 410 Ų buried · 4 hydrogen bonds · protein-protein
Compared structures
- 5ZXI · Co-crystal structure of an Inhibitor in complex with human PPARdelta 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 Q03181
- Elsewhere: RCSB PDB 5ZXI · PDBe 5ZXI · UniProt Q03181
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