3MPM | pdb_00003mpm

LCK complexed with a pyrazolopyrimidine

• PDB DOI: https://doi.org/10.2210/pdb3MPM/pdb

• Classification: TRANSFERASE
• Organism(s): Homo sapiens
• Expression System: Spodoptera frugiperda
• Mutation(s): Yes 


• Deposited: 2010-04-27 Released: 2010-06-02 
• Deposition Author(s): Cowan-Jacob, S.W., Rummel, G.

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.95 Å
• R-Value Free: 
  0.213 (Depositor), 0.225 (DCC) 
• R-Value Work: 
  0.170 (Depositor), 0.196 (DCC) 
• R-Value Observed: 
  0.172 (Depositor) 

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

• PubMed: 20483608 
• DOI: https://doi.org/10.1016/j.bmcl.2010.04.112
• Primary Citation 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.

---

Organizational Affiliation: 
• Novartis Institute of Biomedical Research, Forum 1, Novartis Campus, Basel, Switzerland. [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: 31.12 kDa 
• Atom Count: 2,381 
• Modeled Residue Count: 257 
• Deposited Residue Count: 267 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Tyrosine-protein kinase Lck	A	267	Homo sapiens	Mutation(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 GTEx:  ENSG00000182866

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
5LK	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
EDO	C [auth A]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.95 Å
• R-Value Free:  0.213 (Depositor), 0.225 (DCC) 
• R-Value Work:  0.170 (Depositor), 0.196 (DCC) 
• R-Value Observed: 0.172 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 58.073	α = 90
b = 44.624	β = 90
c = 120.967	γ = 90

Software Package:

Software Name	Purpose
MAR345dtb	data collection
REFMAC	refinement
XDS	data reduction
XSCALE	data scaling
REFMAC	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2010-06-02 
Deposition Author(s): Cowan-Jacob, S.W., Rummel, G.

Revision History  

• 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
• Version 1.4: 2024-02-21
  Changes: Data collection