MolNFT v1 · #75049 · protein
Ppard complexed with a phenoxyacetic acid partial agonist
3PEQ · Peroxisome proliferator-activated receptor delta: “Ppard complexed with a phenoxyacetic acid partial agonist”. X-ray diffraction, 3 ligands (JZR, 3EQ, IOD), 6 pockets (best druggability 0.85). MolNFT v1 #75049 on GenesisL1: 3D…
- PDB
- 3PEQ
- Type
- protein
- Length
- 512 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Peroxisome proliferator-activated receptor delta
- UniProt
- Q03181
- Ligands
- JZR, 3EQ, IOD
- Pockets
- 6 · best druggability 0.85
Structure
x-ray diffraction · 2 distinct chains · 69% helix, 5% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Peroxisome proliferator-activated receptor delta | protein | 255 | 69% helix, 5% strand | Q03181 |
| B | Peroxisome proliferator-activated receptor delta | protein | 257 | 69% helix, 5% strand | Q03181 |
Ligands and binding sites
- JZR · hexyl beta-D-glucopyranoside · ligand · 3 copies · chains A, B
- 3EQ · [(4-{butyl[2-methyl-4'-(methylsulfanyl)biphenyl-3-yl]sulfamoyl}naphthalen-1-yl)oxy]acetic acid · ligand · 2 copies · chains A, B
- IOD · Iodide ion · ion · 6 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 557 | 0.85 | 0.90 | 52 | 3EQ |
| 2 | 643 | 0.85 | 0.89 | 61 | 3EQ, JZR |
| 3 | 93 | 0.44 | 0.79 | 16 | empty |
| 4 | 78 | 0.41 | 0.79 | 15 | empty |
| 5 | 61 | 0.32 | 0.76 | 10 | JZR |
Compared structures
- 3PEQ · PPARd complexed with a phenoxyacetic acid partial agonist · 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 3PEQ · PDBe 3PEQ · UniProt Q03181
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