3B2W | pdb_00003b2w

Crystal structure of pyrimidine amide 11 bound to Lck

• PDB DOI: https://doi.org/10.2210/pdb3B2W/pdb

• Classification: TRANSFERASE
• Organism(s): Homo sapiens
• Expression System: unidentified baculovirus
• Mutation(s): No 


• Deposited: 2007-10-19 Released: 2007-12-18 
• Deposition Author(s): Huang, X.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free: 
  0.308 (Depositor) 
• R-Value Work: 
  0.230 (Depositor) 
• R-Value Observed: 
  0.230 (Depositor) 

Starting Model: experimental

Literature

N-(3-(phenylcarbamoyl)arylpyrimidine)-5-carboxamides as potent and selective inhibitors of Lck: structure, synthesis and SAR.

Deak, H.L., Newcomb, J.R., Nunes, J.J., Boucher, C., Cheng, A.C., DiMauro, E.F., Epstein, L.F., Gallant, P., Hodous, B.L., Huang, X., Lee, J.H., Patel, V.F., Schneider, S., Turci, S.M., Zhu, X.

(2008) Bioorg Med Chem Lett 18: 1172-1176

• PubMed: 18083554 
• DOI: https://doi.org/10.1016/j.bmcl.2007.11.123
• Primary Citation Related Structures: 
  3B2W


• PubMed Abstract: 
  

  N-3-(Phenylcarbamoyl)arylpyrimidine-5-carboxamides are a novel class of selective Lck inhibitors. This series of compounds derives its selectivity from a hydrogen bond with the gatekeeper Thr316 of the enzyme. X-ray co-crystal structural data, structure-activity relationships, and the synthesis of these inhibitors are reported herein.

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Organizational Affiliation: 
• Department of Medicinal Chemistry, Amgen Inc., One Kendall Square, Building 1000, Cambridge, MA 02139, USA. [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: 32.68 kDa 
• Atom Count: 2,248 
• Modeled Residue Count: 261 
• Deposited Residue Count: 277 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Proto-oncogene tyrosine-protein kinase LCK	A	277	Homo sapiens	Mutation(s): 0  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 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
9NH	B [auth A]	N-[5-({[2-fluoro-3-(trifluoromethyl)phenyl]amino}carbonyl)-2-methylphenyl]-4-methoxy-2-[(4-piperazin-1-ylphenyl)amino]pyrimidine-5-carboxamide C31 H29 F4 N7 O3 RZSXAGWVTKQZAS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free:  0.308 (Depositor) 
• R-Value Work:  0.230 (Depositor) 
• R-Value Observed: 0.230 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 45.18	α = 90
b = 75.19	β = 112.35
c = 47.11	γ = 90

Software Package:

Software Name	Purpose
ADSC	data collection
AMoRE	phasing
CNS	refinement
DENZO	data reduction
SCALEPACK	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2007-12-18 
Deposition Author(s): Huang, X.

Revision History  

• Version 1.0: 2007-12-18
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2023-08-30
  Changes: Data collection, Database references, Derived calculations, Refinement description