6PYU

Human PI3Kdelta in complex with Compound 4-2 ((3S)-1'-(cyclopropanecarbonyl)-5-(quinoxalin-6-yl)spiro[indole-3,2'-pyrrolidin]-2(1H)-one)

• PDB DOI: https://doi.org/10.2210/pdb6PYU/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: 2.54 Å
• R-Value Free: 0.292 
• R-Value Work: 0.240 
• R-Value Observed: 0.241 

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: Hetero 2-mer - A1B1 

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

Macromolecule Content

• Total Structure Weight: 137.86 kDa 
• Atom Count: 8,927 
• Modelled Residue Count: 1,090 
• Deposited Residue Count: 1,187 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit delta isoform	A	1,018	Homo sapiens	Mutation(s): 0  Gene Names: PIK3CD EC: 2.7.1.153 (PDB Primary Data), 2.7.1.137 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for O00329 (Homo sapiens) Explore O00329  Go to UniProtKB:  O00329
PHAROS:  O00329 GTEx:  ENSG00000171608

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Phosphatidylinositol 3-kinase regulatory subunit alpha	B	169	Homo sapiens	Mutation(s): 0  Gene Names: PIK3R1, GRB1
UniProt & NIH Common Fund Data Resources
Find proteins for P27986 (Homo sapiens) Explore P27986  Go to UniProtKB:  P27986
PHAROS:  P27986 GTEx:  ENSG00000145675

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
P5V	C [auth A]	(3S)-1'-(cyclopropanecarbonyl)-5-(quinoxalin-6-yl)spiro[indole-3,2'-pyrrolidin]-2(1H)-one C23 H20 N4 O2 PXPGVPPGCPSCSN-QHCPKHFHSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
P5V	BindingDB:  6PYU	IC50: 10 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.54 Å
• R-Value Free: 0.292 
• R-Value Work: 0.240 
• R-Value Observed: 0.241 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 90.439	α = 90
b = 108.587	β = 90
c = 142.279	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
XSCALE	data scaling
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