6OCU

HUMAN PI3KDELTA IN COMPLEX WITH COMPOUND 29


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.77 Å
  • R-Value Free: 0.287 
  • R-Value Work: 0.219 
  • R-Value Observed: 0.221 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history


Literature

Discovery and optimization of heteroaryl piperazines as potent and selective PI3K delta inhibitors.

Zhou, H.McGowan, M.A.Lipford, K.Christopher, M.Fradera, X.Witter, D.Lesburg, C.A.Li, C.Methot, J.L.Lampe, J.Achab, A.Shaffer, L.Goldenblatt, P.Shah, S.Bass, A.Schroeder, G.Chen, D.Zeng, H.Augustin, M.A.Katz, J.D.

(2020) Bioorg Med Chem Lett 30: 126715-126715

  • DOI: https://doi.org/10.1016/j.bmcl.2019.126715
  • Primary Citation of Related Structures:  
    6OCO, 6OCU

  • PubMed Abstract: 

    A high-throughput screening (HTS) campaign identified a class of heteroaryl piperazines with excellent baseline affinity and selectivity for phosphoinositide 3-kinase δ (PI3Kδ) over closely related isoforms. Rapid evaluation and optimization of structure-activity relationships (SAR) for this class, leveraging the modular nature of this scaffold, facilitated development of this hit class into a series of potent and selective inhibitors of PI3Kδ. This effort culminated in the identification of 29, which displayed excellent potency in enzyme and cell-based assays, as well as favorable pharmacokinetic and off-target profiles.


  • Organizational Affiliation

    Department of Discovery Chemistry, Merck & Co., Inc., 33 Avenue Louis Pasteur, Boston, MA 02115, USA. Electronic address: hua_zhou2@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 isoform1,044Homo 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
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Phosphatidylinositol 3-kinase regulatory subunit alpha188Bos taurusMutation(s): 0 
Gene Names: PIK3R1
UniProt
Find proteins for P23727 (Bos taurus)
Explore P23727 
Go to UniProtKB:  P23727
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP23727
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
M5D (Subject of Investigation/LOI)
Query on M5D

Download Ideal Coordinates CCD File 
C [auth A]5-{(3R)-3-methyl-4-[(1R,2R)-2-methylcyclopropane-1-carbonyl]piperazin-1-yl}-3-(1-methyl-1H-pyrazol-4-yl)pyrazine-2-carbonitrile
C19 H23 N7 O
GXEXIUKEWXZCEF-UMVBOHGHSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.77 Å
  • R-Value Free: 0.287 
  • R-Value Work: 0.219 
  • R-Value Observed: 0.221 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 90.998α = 90
b = 109.407β = 90
c = 142.592γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
PDB_EXTRACTdata extraction
XSCALEdata scaling
MOLREPphasing
XDS/XSCALEdata collection

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2019-12-11
    Type: Initial release
  • Version 1.1: 2019-12-18
    Changes: Database references
  • Version 1.2: 2024-03-13
    Changes: Advisory, Data collection, Database references