MolNFT v1 · #152506 · protein
Human ppargamma ligand binding domain complexed with SB1495
6IJR · Peroxisome proliferator-activated receptor gamma: “Human ppargamma ligand binding domain complexed with SB1495”. X-ray diffraction, 1 ligand (A9C), 3 pockets (best druggability 0.85). MolNFT v1 #152506 on GenesisL1: 3D structure…
- PDB
- 6IJR
- Type
- protein
- Length
- 583 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Peroxisome proliferator-activated receptor gamma; 16 mer peptide from nuclear receptor…
- EC
- 2.3.1.48
- UniProt
- P37231, Q15788
- Ligands
- A9C
- Pockets
- 3 · best druggability 0.85
Structure
x-ray diffraction · 4 distinct chains · 63% helix, 4% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Peroxisome proliferator-activated receptor gamma | protein | 281 | 62% helix, 4% strand | P37231 |
| B | 16 mer peptide from nuclear receptor coactivator 1 (EC 2.3.1.48) | protein | 9 | 67% helix, 0% strand | Q15788 |
| C | Peroxisome proliferator-activated receptor gamma | protein | 283 | 64% helix, 5% strand | P37231 |
| D | 16 mer peptide from nuclear receptor coactivator 1 (EC 2.3.1.48) | protein | 10 | 60% helix, 0% strand | Q15788 |
Ligands and binding sites
- A9C · N-{[3-({[(1S,2R)-2-{[(2E)-2-cyano-4,4-dimethylpent-2-enoyl]amino}cyclopentyl]oxy}methyl)phenyl]methyl}-4-[(4-methylpiperazin-1-yl)methyl]benzamide · ligand · 2 copies · chains A, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 607 | 0.85 | 0.90 | 68 | A9C |
| 2 | 640 | 0.85 | 0.89 | 66 | A9C |
| 3 | 87 | 0.34 | 0.74 | 18 | empty |
Interfaces
4 interfaces between chains.
- C–D · 566 Ų buried · 6 hydrogen bonds · protein-protein
- A–B · 534 Ų buried · 4 hydrogen bonds · protein-protein
- A–C · 122 Ų buried · 4 hydrogen bonds · protein-protein
- B–C · 57 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 covalent (covalent ligand).
Compared structures
- 6IJR · Human PPARgamma ligand binding domain complexed with SB1495 · 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 6IJR · PDBe 6IJR · UniProt P37231 · UniProt Q15788
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