6PYS

Human PI3Kalpha in complex with Compound 2-10 ((3S)-3-benzyl-3-methyl-5-[5-(2-methylpyrimidin-5-yl)pyrazolo[1,5-a]pyrimidin-3-yl]-1,3-dihydro-2H-indol-2-one)

• PDB DOI: https://doi.org/10.2210/pdb6PYS/pdb

• Classification: TRANSFERASE/TRANSFERASE INHIBITOR
• Organism(s): Homo sapiens
• Expression System: Spodoptera frugiperda
• Mutation(s): No 


• Deposited: 2019-07-30 Released: 2019-08-28 
• Deposition Author(s): Lesburg, C.A., Augustin, M.A.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.19 Å
• R-Value Free: 0.259 
• R-Value Work: 0.224 
• R-Value Observed: 0.225 

Literature

Design of selective PI3K delta inhibitors using an iterative scaffold-hopping workflow.

Fradera, X., Methot, J.L., Achab, A., Christopher, M., Altman, M.D., Zhou, H., McGowan, M.A., Kattar, S.D., Wilson, K., Garcia, Y., Augustin, M.A., Lesburg, C.A., Shah, S., Goldenblatt, P., Katz, J.D.

(2019) Bioorg Med Chem Lett 29: 2575-2580

• PubMed: 31416665 
• DOI: https://doi.org/10.1016/j.bmcl.2019.08.004
• Primary Citation of Related Structures:  
  6PYR, 6PYS, 6PYU


• PubMed Abstract: 
  

  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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Organizational Affiliation: 

Computational and Structural Chemistry, Merck & Co., Inc., Boston, MA, USA. Electronic address: [e-mail].

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 110.61 kDa 
• Atom Count: 7,558 
• Modelled Residue Count: 890 
• Deposited Residue Count: 945 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit alpha isoform	A	945	Homo sapiens	Mutation(s): 0  Gene Names: PIK3CA EC: 2.7.1.153 (PDB Primary Data), 2.7.11.1 (PDB Primary Data)
UniProt & NIH Common Fund Data Resources
Find proteins for P42336 (Homo sapiens) Explore P42336  Go to UniProtKB:  P42336
PHAROS:  P42336 GTEx:  ENSG00000121879

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
P5J (Subject of Investigation/LOI)	B [auth A]	(3S)-3-benzyl-3-methyl-5-[5-(2-methylpyrimidin-5-yl)pyrazolo[1,5-a]pyrimidin-3-yl]-1,3-dihydro-2H-indol-2-one C27 H22 N6 O KQGDDLRQLMABOG-MHZLTWQESA-N
GOL	C [auth A], D [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.19 Å
• R-Value Free: 0.259 
• R-Value Work: 0.224 
• R-Value Observed: 0.225 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 58.44	α = 90
b = 133.914	β = 90
c = 141.719	γ = 90

Software Package:

Software Name	Purpose
XSCALE	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
XDS	data reduction
REFMAC	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2019-08-28 
Deposition Author(s): Lesburg, C.A., Augustin, M.A.

Revision History  

• Version 1.0: 2019-08-28
  Type: Initial release
  
• Version 1.1: 2019-09-04
  Changes: Data collection, Database references
• Version 1.2: 2024-03-13
  Changes: Advisory, Data collection, Database references