6PYR

Human PI3Kdelta 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)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.21 Å
  • R-Value Free: 0.259 
  • R-Value Work: 0.221 
  • R-Value Observed: 0.222 

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Ligand Structure Quality Assessment 


This is version 1.1 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: 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 ...

    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

    Discovery Chemistry, Merck & Co., Inc., Boston, MA, USA.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit delta isoformA1018Homo sapiensMutation(s): 0 
Gene Names: PIK3CD
EC: 2.7.1.153
UniProt & NIH Common Fund Data Resources
Find proteins for O00329 (Homo sapiens)
Explore O00329 
Go to UniProtKB:  O00329
PHAROS:  O00329
Protein Feature View
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Phosphatidylinositol 3-kinase regulatory subunit alphaB169Homo 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
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
P5J (Subject of Investigation/LOI)
Query on P5J

Download Ideal Coordinates CCD File 
C [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
 Ligand Interaction
Binding Affinity Annotations 
IDSourceBinding Affinity
P5J Binding MOAD:  6PYR IC50: 1 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.21 Å
  • R-Value Free: 0.259 
  • R-Value Work: 0.221 
  • R-Value Observed: 0.222 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 90.471α = 90
b = 108.078β = 90
c = 142.346γ = 90
Software Package:
Software NamePurpose
XSCALEdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
XDSdata reduction
REFMACphasing

Structure Validation

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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