3S1B

The Development of Peptide-based Tools for the Analysis of Angiogenesis


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.90 Å
  • R-Value Free: 0.251 
  • R-Value Work: 0.221 
  • R-Value Observed: 0.222 

wwPDB Validation   3D Report Full Report


This is version 1.0 of the entry. See complete history


Literature

The development of Peptide-based tools for the analysis of angiogenesis.

Fedorova, A.Zobel, K.Gill, H.S.Ogasawara, A.Flores, J.E.Tinianow, J.N.Vanderbilt, A.N.Wu, P.Meng, Y.G.Williams, S.P.Wiesmann, C.Murray, J.Marik, J.Deshayes, K.

(2011) Chem Biol 18: 839-845

  • DOI: https://doi.org/10.1016/j.chembiol.2011.05.011
  • Primary Citation of Related Structures:  
    3S1B, 3S1K

  • PubMed Abstract: 

    Limitations to the application of molecularly targeted cancer therapies are the inability to accurately match patient with effective treatment and the absence of a prompt readout of posttreatment response. Noninvasive agents that rapidly report vascular endothelial growth factor (VEGF) levels using positron emission tomography (PET) have the potential to enhance anti-angiogenesis therapies. Using phage display, two distinct classes of peptides were identified that bind to VEGF with nanomolar affinity and high selectivity. Co-crystal structures of these different peptide classes demonstrate that both bind to the receptor-binding region of VEGF. (18)F-radiolabelling of these peptides facilitated the acquisition of PET images of tumor VEGF levels in a HM7 xenograph model. The images obtained from one 59-residue probe, (18)F-Z-3B, 2 hr postinjection are comparable to those obtained with anti-VEGF antibody B20 72 hr postinjection. Furthermore, VEGF levels in growing SKOV3 tumors were followed using (18)F-Z-3B as a PET probe with VEGF levels increasing with tumor size.


  • Organizational Affiliation

    Department of Early Discovery Biochemistry, Genentech, South San Francisco, CA 94080, USA.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Vascular endothelial growth factor AA [auth V]96Homo sapiensMutation(s): 0 
Gene Names: VEGFVEGFA
UniProt & NIH Common Fund Data Resources
Find proteins for P15692 (Homo sapiens)
Explore P15692 
Go to UniProtKB:  P15692
PHAROS:  P15692
GTEx:  ENSG00000112715 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP15692
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
mini-ZB [auth A]34N/AMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.90 Å
  • R-Value Free: 0.251 
  • R-Value Work: 0.221 
  • R-Value Observed: 0.222 
  • Space Group: P 65 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 70.94α = 90
b = 70.94β = 90
c = 161.288γ = 120
Software Package:
Software NamePurpose
DENZOdata reduction
PHASERphasing
PHENIXrefinement
PDB_EXTRACTdata extraction
HKL-2000data collection
SCALEPACKdata scaling

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2011-08-17
    Type: Initial release