4MBL | pdb_00004mbl

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

• PDB DOI: https://doi.org/10.2210/pdb4MBL/pdb

• Classification: TRANSFERASE/TRANSFERASE INHIBITOR
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2013-08-19 Released: 2013-09-11 
• Deposition Author(s): Azevedo, R., Fischmann, T.O.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.60 Å
• R-Value Free: 
  0.242 (Depositor), 0.246 (DCC) 
• R-Value Work: 
  0.201 (Depositor), 0.204 (DCC) 
• R-Value Observed: 
  0.206 (Depositor) 

Literature

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

• PubMed: 24091081 
• DOI: https://doi.org/10.1016/j.bmcl.2013.08.110
• Primary Citation 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.

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Organizational Affiliation: 
• Department of Chemical Research, Merck Research Laboratories, 2015 Galloping Hill Road, Kenilworth, NJ 07033, United States. Electronic address: [e-mail].

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 34.2 kDa 
• Atom Count: 2,257 
• Modeled Residue Count: 274 
• Deposited Residue Count: 293 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Serine/threonine-protein kinase pim-1	A	293	Homo sapiens	Mutation(s): 0  Gene Names: PIM1 EC: 2.7.11.1
UniProt & NIH Common Fund Data Resources
Find proteins for P11309 (Homo sapiens) Explore P11309  Go to UniProtKB:  P11309
PHAROS:  P11309 GTEx:  ENSG00000137193

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
26L	B [auth A]	(1R,2R)-N-[3-(naphthalen-2-yl)pyrazolo[1,5-a]pyrimidin-5-yl]cyclohexane-1,2-diamine C22 H23 N5 LODPYXJMYAQIRB-WOJBJXKFSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
26L	BindingDB:  4MBL	IC50: 2.9 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.60 Å
• R-Value Free:  0.242 (Depositor), 0.246 (DCC) 
• R-Value Work:  0.201 (Depositor), 0.204 (DCC) 
• R-Value Observed: 0.206 (Depositor) 

Space Group: P 6₅

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 98.56	α = 90
b = 98.56	β = 90
c = 80.859	γ = 120

Software Package:

Software Name	Purpose
CrystalClear	data collection
AMoRE	phasing
BUSTER	refinement
d*TREK	data reduction
d*TREK	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2013-09-11 
Deposition Author(s): Azevedo, R., Fischmann, T.O.

Revision History  

• Version 1.0: 2013-09-11
  Type: Initial release
  
• Version 1.1: 2013-10-30
  Changes: Database references
• Version 1.2: 2024-02-28
  Changes: Data collection, Database references, Derived calculations