1SKJ

COCRYSTAL STRUCTURE OF UREA-SUBSTITUTED PHOSPHOPEPTIDE COMPLEX


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.275 
  • R-Value Work: 0.200 
  • R-Value Observed: 0.200 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


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

  • DOI: 10.1021/jm970402q
  • Primary Citation of 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 ...

    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.


    Related Citations: 
    • Binding of a High Affinity Phosphotyrosyl Peptide to the Src Sh2 Domain: Crystal Structures of the Complexed and Peptide-Free Forms
      Waksman, G., Shoelson, S.E., Pant, N., Cowburn, D., Kuriyan, J.
      (1993) Cell 72: 779

    Organizational Affiliation

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



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
PP60 V-SRC TYROSINE KINASE TRANSFORMING PROTEIN A113Rous sarcoma virusMutation(s): 0 
EC: 2.7.1.112 (PDB Primary Data), 2.7.10.2 (UniProt)
Find proteins for P00524 (Avian leukosis virus RSA)
Explore P00524 
Go to UniProtKB:  P00524
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
UR2
Query on UR2

Download Ideal Coordinates CCD File 
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
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
UR2IC50:  7000   nM  BindingDB
UR2IC50:  7000   nM  Binding MOAD
UR2IC50 :  7000   nM  PDBBind
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.275 
  • R-Value Work: 0.200 
  • R-Value Observed: 0.200 
  • Space Group: P 61
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 74.4α = 90
b = 74.4β = 90
c = 38.8γ = 120
Software Package:
Software NamePurpose
X-PLORmodel building
X-PLORrefinement
XDSdata reduction
XDSdata scaling
X-PLORphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

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