MolNFT v1 · #146233 · protein
Crystal structure of ppar gamma in complex with NMP422
6DBH · Peroxisome proliferator-activated receptor gamma: “Crystal structure of ppar gamma in complex with NMP422”. X-ray diffraction, 2 ligands (G3S, CL), 7 pockets (best druggability 0.84). MolNFT v1 #146233 on GenesisL1: 3D structure…
- PDB
- 6DBH
- Type
- protein
- Length
- 530 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Peroxisome proliferator-activated receptor gamma
- UniProt
- P37231
- Ligands
- G3S, CL
- Pockets
- 7 · best druggability 0.84
Structure
x-ray diffraction · 2 distinct chains · 66% helix, 5% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Peroxisome proliferator-activated receptor gamma | protein | 271 | 66% helix, 4% strand | P37231 |
| B | Peroxisome proliferator-activated receptor gamma | protein | 259 | 65% helix, 5% strand | P37231 |
Ligands and binding sites
- G3S · 4-{2-[(2,3-dioxo-1-pentyl-2,3-dihydro-1H-indol-5-yl) sulfanyl]ethyl}benzoic acid · ligand · 2 copies · chains A, B
- CL · Chloride ion · ion · 3 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 529 | 0.84 | 0.90 | 56 | G3S, CL |
| 2 | 342 | 0.82 | 0.92 | 38 | G3S, CL |
| 3 | 401 | 0.64 | 0.78 | 44 | empty |
| 4 | 159 | 0.63 | 0.85 | 28 | empty |
| 5 | 273 | 0.60 | 0.79 | 37 | empty |
Interfaces
1 interface between chains.
- A–B · 917 Ų buried · 2 hydrogen bonds · protein-protein
Compared structures
- 6DBH · Crystal structure of PPAR gamma in complex with NMP422 · 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
- Elsewhere: RCSB PDB 6DBH · PDBe 6DBH · UniProt P37231
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