6PYU image
Deposition Date 2019-07-30
Release Date 2019-08-28
Last Version Date 2024-03-13
Entry Detail
PDB ID:
6PYU
Keywords:
TRANSFERASE/TRANSFERASE INHIBITOR
Title:
Human PI3Kdelta in complex with Compound 4-2 ((3S)-1'-(cyclopropanecarbonyl)-5-(quinoxalin-6-yl)spiro[indole-3,2'-pyrrolidin]-2(1H)-one)
Biological Source:
Source Organism:
Homo sapiens (Taxon ID: 9606)
Host Organism:
Spodoptera frugiperda
Method Details:
Experimental Method:
X-RAY DIFFRACTION
Resolution:
2.54 Å
R-Value Free:
0.29
R-Value Work:
0.23
R-Value Observed:
0.24
Space Group:
P 21 21 21
6PYU validation report
Macromolecular Entities
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit delta isoform
Gene (Uniprot):PIK3CD
Chain IDs:A
Chain Length:1018
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:O00329 Pfam ID:PF02192, PF00794, PF00792, PF00613, PF00454 EC:2.7.1.137
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Phosphatidylinositol 3-kinase regulatory subunit alpha
Gene (Uniprot):PIK3R1
Chain IDs:B
Chain Length:169
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:P27986 Pfam ID:PF16454 EC:2.7.1.153
Ligand Molecules
P5V
Primary Citation
Design of selective PI3K delta inhibitors using an iterative scaffold-hopping workflow.
Bioorg.Med.Chem.Lett. 29 2575 2580 (2019)
PMID: 31416665 DOI: 10.1016/j.bmcl.2019.08.004

Abstact

PI3Kδ mediates key immune cell signaling pathways and is a target of interest for multiple indications in immunology and oncology. Here we report a structure-based scaffold-hopping strategy for the design of chemically diverse PI3Kδ inhibitors. Using this strategy, we identified several scaffolds that can be combined to generate new PI3Kδ inhibitors with high potency and isoform selectivity. In particular, an oxindole-based scaffold was found to impart exquisite selectivity when combined with several hinge binding motifs.

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Disease

Primary Citation of related structures
6PYU