Discovery of Pyrazolo[1,5a]pyrimidine-based Pim1 Inhibitors

Experimental Data Snapshot

  • Resolution: 2.60 Å
  • R-Value Free: 0.242 
  • R-Value Work: 0.201 
  • R-Value Observed: 0.206 

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Ligand Structure Quality Assessment 

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Discovery of pyrazolo[1,5-a]pyrimidine-based Pim inhibitors: A template-based approach.

Dwyer, M.P.Keertikar, K.Paruch, K.Alvarez, C.Labroli, M.Poker, C.Fischmann, T.O.Mayer-Ezell, R.Bond, R.Wang, Y.Azevedo, R.Guzi, T.J.

(2013) Bioorg Med Chem Lett 23: 6178-6182

  • DOI: 10.1016/j.bmcl.2013.08.110
  • Primary Citation of Related Structures:  
    4MBI, 4MBL

  • PubMed Abstract: 
  • The synthesis and hit-to-lead SAR development from a pyrazolo[1,5-a]pyrimidine-derived hit 5 to the identification of a series of potent, pan-Pim inhibitors such as 11j are described.

    Organizational Affiliation

    Department of Chemical Research, Merck Research Laboratories, 2015 Galloping Hill Road, Kenilworth, NJ 07033, United States. Electronic address: michael.dwyer@merck.com.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Serine/threonine-protein kinase pim-1A293Homo sapiensMutation(s): 0 
Gene Names: PIM1
UniProt & NIH Common Fund Data Resources
Find proteins for P11309 (Homo sapiens)
Explore P11309 
Go to UniProtKB:  P11309
PHAROS:  P11309
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP11309
Protein Feature View
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
Query on 26L

Download Ideal Coordinates CCD File 
B [auth A](1R,2R)-N-[3-(naphthalen-2-yl)pyrazolo[1,5-a]pyrimidin-5-yl]cyclohexane-1,2-diamine
C22 H23 N5
 Ligand Interaction
Binding Affinity Annotations 
IDSourceBinding Affinity
26L PDBBind:  4MBL IC50: 2.9 (nM) from 1 assay(s)
BindingDB:  4MBL IC50: 2.9 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Resolution: 2.60 Å
  • R-Value Free: 0.242 
  • R-Value Work: 0.201 
  • R-Value Observed: 0.206 
  • Space Group: P 65
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 98.56α = 90
b = 98.56β = 90
c = 80.859γ = 120
Software Package:
Software NamePurpose
CrystalCleardata collection
d*TREKdata reduction
d*TREKdata scaling

Structure Validation

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Ligand Structure Quality Assessment 

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2013-09-11
    Type: Initial release
  • Version 1.1: 2013-10-30
    Changes: Database references