1CJ1

GROWTH FACTOR RECEPTOR BINDING PROTEIN SH2 DOMAIN (HUMAN) COMPLEXED WITH A PHOSPHOTYROSYL DERIVATIVE


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.00 Å
  • R-Value Free: 0.317 
  • R-Value Work: 0.305 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 1.4 of the entry. See complete history


Literature

Structure-based design, synthesis, and X-ray crystallography of a high-affinity antagonist of the Grb2-SH2 domain containing an asparagine mimetic.

Furet, P.Garcia-Echeverria, C.Gay, B.Schoepfer, J.Zeller, M.Rahuel, J.

(1999) J Med Chem 42: 2358-2363

  • DOI: https://doi.org/10.1021/jm991013u
  • Primary Citation of Related Structures:  
    1CJ1

  • PubMed Abstract: 

    Previous efforts in the search for molecules capable of blocking the associations between the activated tyrosine kinase growth factor receptors and the SH2 domain of Grb2 had resulted in the identification of 3-amino-Z-pTyr-Ac6c-Asn-NH2, a high-affinity and selective antagonist of this SH2 domain. In the present paper, we report the successful replacement of asparagine in this compound by a beta-amino acid mimetic, which brings us closer to our objective of identifying a Grb2-SH2 antagonist suitable for pharmacological investigations.


  • Organizational Affiliation

    Oncology Research Department, Novartis Pharma Inc., CH-4002 Basel, Switzerland. pascal.furet@pharma.novartis.com


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
PROTEIN (GROWTH FACTOR RECEPTOR-BOUND PROTEIN 2)
A, B, C, D, E
A, B, C, D, E, F, G, H, I, J, K, L
96Homo sapiensMutation(s): 0 
UniProt & NIH Common Fund Data Resources
Find proteins for P62993 (Homo sapiens)
Explore P62993 
Go to UniProtKB:  P62993
PHAROS:  P62993
GTEx:  ENSG00000177885 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP62993
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
C78
Query on C78

Download Ideal Coordinates CCD File 
M [auth A]
N [auth B]
O [auth C]
P [auth D]
Q [auth E]
M [auth A],
N [auth B],
O [auth C],
P [auth D],
Q [auth E],
R [auth F],
S [auth G],
T [auth H],
U [auth I],
V [auth J],
W [auth K],
X [auth L]
[1-[1-(6-CARBAMOYL-CYCLOHEX-2-ENYLCARBAMOYL)-CYCLOHEXYLCARBAMOYL]-2-(4-PHOSPHONOOXY-PHENYL)- ETHYL]-CARBAMIC ACID 3-AMINOBENZYLESTER
C31 H42 N5 O9 P
SLNOMHLVQNIGRT-NXCFDTQHSA-N
Binding Affinity Annotations 
IDSourceBinding Affinity
C78 PDBBind:  1CJ1 IC50: 1.6 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.00 Å
  • R-Value Free: 0.317 
  • R-Value Work: 0.305 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 73.8α = 90
b = 93.3β = 90
c = 232.8γ = 90
Software Package:
Software NamePurpose
AMoREphasing
X-PLORrefinement
XDSdata reduction
AUTOMARdata reduction

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

  • Released Date: 1999-12-22 
  • Deposition Author(s): Rahuel, J.

Revision History  (Full details and data files)

  • Version 1.0: 1999-12-22
    Type: Initial release
  • Version 1.1: 2008-04-26
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2017-10-04
    Changes: Refinement description
  • Version 1.4: 2023-08-02
    Changes: Database references, Derived calculations, Refinement description