MolNFT v1 · #139677 · protein
Co-crystal structure of inhibitor compound in complex with human ppardelta lbd
5XMX · Peroxisome proliferator-activated receptor delta: “Co-crystal structure of inhibitor compound in complex with human ppardelta lbd”. X-ray diffraction, 1 ligand (89L), 6 pockets (best druggability 0.84). MolNFT v1 #139677 on…
- PDB
- 5XMX
- Type
- protein
- Length
- 502 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Peroxisome proliferator-activated receptor delta
- UniProt
- Q03181
- Ligands
- 89L
- Pockets
- 6 · best druggability 0.84
Structure
x-ray diffraction · 2 distinct chains · 71% helix, 5% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Peroxisome proliferator-activated receptor delta | protein | 257 | 70% helix, 5% strand | Q03181 |
| B | Peroxisome proliferator-activated receptor delta | protein | 245 | 71% helix, 5% strand | Q03181 |
Ligands and binding sites
- 89L · (E)-6-[2-[[[4-(furan-2-yl)phenyl]carbonyl-methyl-amino]methyl]phenoxy]-4-methyl-hex-4-enoic acid · ligand · 2 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 | 491 | 0.84 | 0.90 | 51 | 89L |
| 2 | 511 | 0.81 | 0.87 | 51 | 89L |
| 3 | 96 | 0.40 | 0.77 | 15 | empty |
| 4 | 70 | 0.36 | 0.77 | 15 | empty |
| 5 | 88 | 0.36 | 0.75 | 16 | empty |
Interfaces
1 interface between chains.
- A–B · 387 Ų buried · 5 hydrogen bonds · protein-protein
Compared structures
- 5XMX · Co-crystal structure of Inhibitor compound 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 5XMX · PDBe 5XMX · UniProt Q03181
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