Research workbench
Human ppargamma ligand binding dmain complexed with SB1453 in a covalent bonded form
Analyse Human ppargamma ligand binding dmain complexed with SB1453 in a covalent bonded… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5DVC
- Type
- protein
- Length
- 279 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
- T53
- Pockets
- 2 · best druggability 0.81
Structure
x-ray diffraction · 2 distinct chains · 68% helix, 4% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Peroxisome proliferator-activated receptor gamma | protein | 268 | 68% helix, 4% strand | P37231 |
| B | Nuclear receptor coactivator 1 (EC 2.3.1.48) | protein | 11 | 73% helix, 0% strand | Q15788 |
Ligands and binding sites
- T53 · N-[2-({3-[({4-[(4-methylpiperazin-1-yl)methyl]benzoyl}amino)methyl]benzyl}oxy)phenyl]-3-nitrobenzamide · 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 | 408 | 0.81 | 0.89 | 55 | T53 |
| 2 | 63 | 0.28 | 0.73 | 11 | empty |
Interfaces
1 interface between chains.
- A–B · 573 Ų buried · 9 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 covalent (covalent ligand).
Compared structures
- 5DVC · Human PPARgamma ligand binding dmain complexed with SB1453 in a covalent bonded form · 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 5DVC · PDBe 5DVC · UniProt P37231 · UniProt Q15788
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