6PYU

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


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 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history


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

  • 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.


  • Organizational Affiliation

    Computational and Structural Chemistry, Merck & Co., Inc., Boston, MA, USA. Electronic address: xavier.fradera@merck.com.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit delta isoform1,018Homo sapiensMutation(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 Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO00329
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Phosphatidylinositol 3-kinase regulatory subunit alpha169Homo sapiensMutation(s): 0 
Gene Names: PIK3R1GRB1
UniProt & NIH Common Fund Data Resources
Find proteins for P27986 (Homo sapiens)
Explore P27986 
Go to UniProtKB:  P27986
PHAROS:  P27986
GTEx:  ENSG00000145675 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP27986
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
P5V
Query on P5V

Download Ideal Coordinates CCD File 
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 
IDSourceBinding 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 = 90.439α = 90
b = 108.587β = 90
c = 142.279γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
XSCALEdata scaling
PDB_EXTRACTdata extraction
XDSdata reduction
REFMACphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • 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