MolNFT v1 · #140344 · protein

Human peroxisome proliferator-activated receptor (ppar) delta in complexed with a potent and selective agonist

5Y7X · Peroxisome proliferator-activated receptor delta: “Human peroxisome proliferator-activated receptor (ppar) delta in complexed with a potent and selective agonist”. X-ray diffraction, 4 ligands (8RR, JZR, K), 5 pockets (best…

PDB: 5Y7X
Type: protein
Length: 520 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Peroxisome proliferator-activated receptor delta
UniProt: Q03181
Ligands: 8RR, JZR, K, CL
Pockets: 5 · best druggability 0.83

Structure

x-ray diffraction · 2 distinct chains · 67% helix, 5% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Peroxisome proliferator-activated receptor delta	protein	258	69% helix, 5% strand	Q03181
B	Peroxisome proliferator-activated receptor delta	protein	262	66% helix, 5% strand	Q03181

Ligands and binding sites

8RR · 2-[2-methyl-4-[[4-methyl-2-[4-(trifluoromethyl)phenyl]-1,3-selenazol-5-yl]methylsulfanyl]phenoxy]ethanoic acid · ligand · 2 copies · chains A, B
JZR · hexyl beta-D-glucopyranoside · ligand · 2 copies · chains A, B
K · Potassium ion · metal · chains A
CL · Chloride ion · ion · 2 copies · chains A, B
PGO · S-1,2-propanediol · additive · chains A

Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.

Pockets

5 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	518	0.83	0.89	51	8RR
2	506	0.82	0.88	50	8RR
3	375	0.73	0.84	38	JZR
4	193	0.51	0.77	23	CL
5	85	0.42	0.79	13	empty

Interfaces

1 interface between chains.

A–B · 738 Å² buried · 0 hydrogen bonds · protein-protein

Compared structures

5Y7X · Human Peroxisome proliferator-activated receptor (PPAR) delta in complexed with a potent… · 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 5Y7X · PDBe 5Y7X · UniProt Q03181

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