6OCO

HUMAN PI3KDELTA IN COMPLEX WITH COMPOUND 6


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.58 Å
  • R-Value Free: 0.296 
  • R-Value Work: 0.259 
  • R-Value Observed: 0.260 

wwPDB Validation 3D Report Full Report


This is version 1.1 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: 10.1016/j.bmcl.2019.126715
  • Structures With Same Primary Citation

  • 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 struc ...

    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.



Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit delta isoformA1015Homo sapiensMutation(s): 0 
Gene Names: PIK3CD
EC: 2.7.1.153
Find proteins for O00329 (Homo sapiens)
Explore O00329 
Go to UniProtKB:  O00329
NIH Common Fund Data Resources
PHAROS  O00329
Protein Feature View
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  • Reference Sequence

Find similar proteins by: Sequence  |  Structure

Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Phosphatidylinositol 3-kinase regulatory subunit alphaB170Bos taurusMutation(s): 0 
Gene Names: PIK3R1
Find proteins for P23727 (Bos taurus)
Explore P23727 
Go to UniProtKB:  P23727
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
M5V
Query on M5V

Download CCD File 
A
4-[(1S,4S)-5-(3-chlorophenyl)-2,5-diazabicyclo[2.2.1]heptan-2-yl]-2-(pyridin-3-yl)pyrimidine-5-carbonitrile
C21 H17 Cl N6
LYMCCCUAFBZMES-OALUTQOASA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.58 Å
  • R-Value Free: 0.296 
  • R-Value Work: 0.259 
  • R-Value Observed: 0.260 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 91.017α = 90
b = 108.981β = 90
c = 142.394γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
XSCALEdata scaling
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2019-12-11
    Type: Initial release
  • Version 1.1: 2019-12-18
    Changes: Database references