MolNFT v1 · #140501 · protein
Human ppargamma ligand binding domain complexed with rosiglitazone
5YCP · Peroxisome proliferator-activated receptor gamma: “Human ppargamma ligand binding domain complexed with rosiglitazone”. X-ray diffraction, 1 ligand (BRL), 2 pockets (best druggability 0.77). MolNFT v1 #140501 on GenesisL1: 3D…
- PDB
- 5YCP
- Type
- protein
- Length
- 274 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Peroxisome proliferator-activated receptor gamma; Nuclear receptor coactivator 1
- EC
- 2.3.1.48
- UniProt
- P37231, Q15788
- Ligands
- BRL
- Pockets
- 2 · 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 | 263 | 67% helix, 5% strand | P37231 |
| B | Nuclear receptor coactivator 1 (EC 2.3.1.48) | protein | 11 | 73% helix, 0% strand | Q15788 |
Ligands and binding sites
- BRL · 2,4-thiazolidiinedione, 5-[[4-[2-(methyl-2-pyridinylamino)ethoxy]phenyl]methyl]-(9CL) · ligand · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 479 | 0.77 | 0.84 | 54 | BRL |
| 2 | 55 | 0.26 | 0.73 | 15 | empty |
Interfaces
1 interface between chains.
- A–B · 621 Ų buried · 5 hydrogen bonds · protein-protein
Compared structures
- 5YCP · Human PPARgamma ligand binding domain complexed with Rosiglitazone · 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
- Every structure of UniProt Q15788
- Elsewhere: RCSB PDB 5YCP · PDBe 5YCP · UniProt P37231 · UniProt Q15788
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