1SKJ | pdb_00001skj

COCRYSTAL STRUCTURE OF UREA-SUBSTITUTED PHOSPHOPEPTIDE COMPLEX

• PDB DOI: https://doi.org/10.2210/pdb1SKJ/pdb

• Classification: TYROSINE-PROTEIN KINASE
• Organism(s): Rous sarcoma virus
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 1997-09-18 Released: 1998-02-25 
• Deposition Author(s): Holland, D.R., Rubin, J.R.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 
  0.275 (Depositor) 
• R-Value Work: 
  0.200 (Depositor), 0.229 (DCC) 
• R-Value Observed: 
  0.200 (Depositor) 

Starting Model: experimental

Literature

Design, synthesis, and cocrystal structure of a nonpeptide Src SH2 domain ligand.

Plummer, M.S., Holland, D.R., Shahripour, A., Lunney, E.A., Fergus, J.H., Marks, J.S., McConnell, P., Mueller, W.T., Sawyer, T.K.

(1997) J Med Chem 40: 3719-3725

• PubMed: 9371236 
• DOI: https://doi.org/10.1021/jm970402q
• Primary Citation Related Structures: 
  1SKJ


• PubMed Abstract: 
  

  The specific association of an SH2 domain with a phosphotyrosine (pTyr)-containing sequence of another protein precipitates a cascade of intracellular molecular interactions (signals) which effect a wide range of intracellular processes. The nonreceptor tyrosine kinase Src, which has been associated with breast cancer and osteoporosis, contains an SH2 domain. Inhibition of Src SH2-phosphoprotein interactions by small molecules will aid biological proof-of-concept studies which may lead to the development of novel therapeutic agents. Structure-based design efforts have focused on reducing the size and charge of Src SH2 ligands while increasing their ability to penetrate cells and reach the intracellular Src SH2 domain target. In this report we describe the synthesis, binding affinity, and Src SH2 cocrystal structure of a small, novel, nonpeptide, urea-containing SH2 domain ligand.

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Organizational Affiliation: 
• Department of Chemistry, Parke-Davis Pharmaceutical Research Division, Warner-Lambert Company, Ann Arbor, Michigan 48105, USA.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 13.48 kDa 
• Atom Count: 919 
• Modeled Residue Count: 102 
• Deposited Residue Count: 113 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
PP60 V-SRC TYROSINE KINASE TRANSFORMING PROTEIN	A	113	Rous sarcoma virus	Mutation(s): 0  EC: 2.7.1.112 (PDB Primary Data), 2.7.10.2 (UniProt)
UniProt
Find proteins for P00524 (Rous sarcoma virus subgroup A (strain Schmidt-Ruppin)) Explore P00524  Go to UniProtKB:  P00524

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
UR2	B [auth A]	4-[3-CARBOXYMETHYL-3-(4-PHOSPHONOOXY-BENZYL)-UREIDO]-4-[(3-CYCLOHEXYL-PROPYL)-METHYL-CARBAMOYL]BUTYRIC ACID C25 H38 N3 O10 P JSBQUMXQEBZYPW-NRFANRHFSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free:  0.275 (Depositor) 
• R-Value Work:  0.200 (Depositor), 0.229 (DCC) 
• R-Value Observed: 0.200 (Depositor) 

Space Group: P 6₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 74.4	α = 90
b = 74.4	β = 90
c = 38.8	γ = 120

Software Package:

Software Name	Purpose
X-PLOR	model building
X-PLOR	refinement
XDS	data reduction
XDS	data scaling
X-PLOR	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 1998-02-25 
Deposition Author(s): Holland, D.R., Rubin, J.R.

Revision History  

• Version 1.0: 1998-02-25
  Type: Initial release
  
• Version 1.1: 2008-03-03
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2023-08-09
  Changes: Database references, Derived calculations, Other, Refinement description
• Version 1.4: 2024-05-22
  Changes: Data collection