3MPM

LCK complexed with a pyrazolopyrimidine

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.95 Å
  • R-Value Free: 0.213 
  • R-Value Work: 0.170 
  • R-Value Observed: 0.172 

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Ligand Structure Quality Assessment 


This is version 1.3 of the entry. See complete history. 


Literature

New pyrazolo[1,5a]pyrimidines as orally active inhibitors of Lck.

Gommermann, N., Buehlmayer, P., von Matt, A., Breitenstein, W., Masuya, K., Pirard, B., Furet, P., Cowan-Jacob, S.W., Weckbecker, G.

(2010) Bioorg Med Chem Lett 20: 3628-3631

  • DOI: 10.1016/j.bmcl.2010.04.112
  • Primary Citation of Related Structures:  
    3MPM

  • PubMed Abstract: 

    • A novel series of pyrazolo[1,5a]pyrimidines was optimized to target lymphocyte-specific kinase (Lck). An efficient synthetic route was developed and SAR studies toward activity and selectivity are described, leading to Lck inhibitors with enzymatic, cellular and in vivo potency ...

    A novel series of pyrazolo[1,5a]pyrimidines was optimized to target lymphocyte-specific kinase (Lck). An efficient synthetic route was developed and SAR studies toward activity and selectivity are described, leading to Lck inhibitors with enzymatic, cellular and in vivo potency.

    Organizational Affiliation: 

    Novartis Institute of Biomedical Research, Forum 1, Novartis Campus, Basel, Switzerland. nina.gommermann@novartis.com



Macromolecules
Find similar proteins by: 
(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Tyrosine-protein kinase LckA267Homo sapiensMutation(s): 1 
Gene Names: LCK
EC: 2.7.10.2
UniProt & NIH Common Fund Data Resources
Find proteins for P06239 (Homo sapiens)
Explore P06239 
Go to UniProtKB:  P06239
PHAROS:  P06239
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP06239
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
5LK
Query on 5LK
Download Ideal Coordinates CCD File 
B [auth A]4-{(6R,7R)-7-amino-3-[3-(4-methylpiperazin-1-yl)phenyl]-6,7-dihydropyrazolo[1,5-a]pyrimidin-6-yl}phenol
C23 H26 N6 O
KIMZUJNGIVVWNZ-RBBKRZOGSA-N		 Ligand Interaction
EDO
Query on EDO
Download Ideal Coordinates CCD File 
C [auth A]1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N		 Ligand Interaction
Binding Affinity Annotations 
IDSourceBinding Affinity
5LK PDBBind:  3MPM IC50: 30 (nM) from 1 assay(s)
Binding MOAD:  3MPM IC50: 30 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.95 Å
  • R-Value Free: 0.213 
  • R-Value Work: 0.170 
  • R-Value Observed: 0.172 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 58.073α = 90
b = 44.624β = 90
c = 120.967γ = 90
Software Package:
Software NamePurpose
MAR345dtbdata collection
REFMACrefinement
XDSdata reduction
XSCALEdata scaling
REFMACphasing

Structure Validation

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Ligand Structure Quality Assessment 


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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2010-06-02
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2018-03-07
    Changes: Data collection
  • Version 1.3: 2021-10-06
    Changes: Database references, Derived calculations