1IJR

Crystal structure of LCK SH2 complexed with nonpeptide phosphotyrosine mimetic

• PDB DOI: https://doi.org/10.2210/pdb1IJR/pdb

• Classification: TRANSFERASE/SIGNALING PROTEIN
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2001-04-27 Released: 2002-05-01 
• Deposition Author(s): Kawahata, N.H., Yang, M.H., Luke, G.P., Shakespeare, W.C., Sundaramoorthi, R.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free: 0.280 
• R-Value Work: 0.230 

Literature

A novel phosphotyrosine mimetic 4'-carboxymethyloxy-3'-phosphonophenylalanine (Cpp): exploitation in the design of nonpeptide inhibitors of pp60(Src) SH2 domain.

Kawahata, N., Yang, M.G., Luke, G.P., Shakespeare, W.C., Sundaramoorthi, R., Wang, Y., Johnson, D., Merry, T., Violette, S., Guan, W., Bartlett, C., Smith, J., Hatada, M., Lu, X., Dalgarno, D.C., Eyermann, C.J., Bohacek, R.S., Sawyer, T.K.

(2001) Bioorg Med Chem Lett 11: 2319-2323

• PubMed: 11527723 
• DOI: https://doi.org/10.1016/s0960-894x(01)00446-2
• Primary Citation of Related Structures:  
  1IJR


• PubMed Abstract: 
  

  The novel phosphotyrosine (pTyr) mimetic 4'-carboxymethyloxy-3'-phosphonophenylalanine (Cpp) has been designed and incorporated into a series of nonpeptide inhibitors of the SH2 domain of pp60(c-Src) (Src) tyrosine kinase. A 2.2 A X-ray crystal structure of 1a bound to a mutant form of Lck SH2 domain provides insight regarding the structure-activity relationships and supports the design concept of this new pTyr mimetic.

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Organizational Affiliation: 

ARIAD Pharmaceuticals, Inc., Cambridge, MA 02139-4234, USA.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 12.45 kDa 
• Atom Count: 877 
• Modelled Residue Count: 104 
• Deposited Residue Count: 104 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
PROTO-ONCOGENE TYROSINE-PROTEIN KINASE LCK	A	104	Homo sapiens	Mutation(s): 0  EC: 2.7.1.112 (PDB Primary Data), 2.7.10.2 (UniProt)
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
CC0	B [auth A]	(4-{2-ACETYLAMINO-2-[1-(3-CARBAMOYL-4-CYCLOHEXYLMETHOXY-PHENYL)-ETHYLCARBAMOYL}-ETHYL}-2-PHOSPHONO-PHENOXY)-ACETIC ACID C29 H38 N3 O10 P FXUGQWABROMTDA-SBUREZEXSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
CC0	PDBBind:  1IJR	IC50: 3600 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free: 0.280 
• R-Value Work: 0.230 
• Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 61.6	α = 90
b = 61.6	β = 90
c = 93.5	γ = 90

Software Package:

Software Name	Purpose
AMoRE	phasing
X-PLOR	refinement
DENZO	data reduction
SCALEPACK	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2002-05-01 
Deposition Author(s): Kawahata, N.H., Yang, M.H., Luke, G.P., Shakespeare, W.C., Sundaramoorthi, R.

Revision History  

• Version 1.0: 2002-05-01
  Type: Initial release
  
• Version 1.1: 2008-04-27
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2024-02-07
  Changes: Data collection, Database references, Derived calculations