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 

Starting Model: experimental
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This is version 1.4 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: https://doi.org/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 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.


  • 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)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
PP60 V-SRC TYROSINE KINASE TRANSFORMING PROTEIN113Rous sarcoma virusMutation(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
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP00524
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
UR2
Query on UR2

Download Ideal Coordinates CCD File 
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
Binding Affinity Annotations 
IDSourceBinding Affinity
UR2 PDBBind:  1SKJ IC50: 7000 (nM) from 1 assay(s)
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

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • 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