Research workbench
Human ppar gamma ligand binding domain in complex with JKPL35
Analyse Human ppar gamma ligand binding domain in complex with JKPL35 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3VJH
- Type
- protein
- Length
- 507 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Peroxisome proliferator-activated receptor gamma
- UniProt
- P37231
- Ligands
- J35
- Pockets
- 5 · best druggability 0.81
Structure
x-ray diffraction · 2 distinct chains · 69% helix, 5% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Peroxisome proliferator-activated receptor gamma | protein | 261 | 69% helix, 5% strand | P37231 |
| B | Peroxisome proliferator-activated receptor gamma | protein | 246 | 69% helix, 5% strand | P37231 |
Ligands and binding sites
- J35 · (2S)-2-[4-methoxy-3-({[4-(trifluoromethyl)benzoyl]amino}methyl)benzyl]pentanoic acid · ligand · 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, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 630 | 0.81 | 0.85 | 62 | J35 |
| 2 | 539 | 0.76 | 0.83 | 59 | empty |
| 3 | 346 | 0.61 | 0.78 | 43 | empty |
| 4 | 91 | 0.61 | 0.89 | 20 | empty |
| 5 | 166 | 0.51 | 0.78 | 24 | empty |
Interfaces
1 interface between chains.
- A–B · 1092 Ų buried · 15 hydrogen bonds · protein-protein
Compared structures
- 3VJH · Human PPAR GAMMA ligand binding domain in complex with JKPL35 · 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 3VJH · PDBe 3VJH · UniProt P37231
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