1SKJ

COCRYSTAL STRUCTURE OF UREA-SUBSTITUTED PHOSPHOPEPTIDE COMPLEX


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2 Å
  • R-Value Free: 0.275 
  • R-Value Work: 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

  • 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 nonrecep ...

    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: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
PP60 V-SRC TYROSINE KINASE TRANSFORMING PROTEIN
A
113Avian leukosis virus RSAMutation(s): 0 
Gene Names: V-SRC
EC: 2.7.10.2
Find proteins for P00524 (Avian leukosis virus RSA)
Go to UniProtKB:  P00524
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
UR2
Query on UR2

Download SDF File 
Download 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 (97) BINDINGDB
UR2IC50: 7000 nM BINDINGMOAD
UR2IC50: 7000 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2 Å
  • R-Value Free: 0.275 
  • R-Value Work: 0.200 
  • Space Group: P 61
Unit Cell:
Length (Å)Angle (°)
a = 74.400α = 90.00
b = 74.400β = 90.00
c = 38.800γ = 120.00
Software Package:
Software NamePurpose
X-PLORmodel building
XDSdata reduction
XDSdata scaling
X-PLORrefinement
X-PLORphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1998-02-25
    Type: Initial release
  • Version 1.1: 2008-03-03
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance