6LUN

NN2101 Antibody Fab fragment


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 0.210 
  • R-Value Work: 0.165 
  • R-Value Observed: 0.167 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Development and characterization of a fully human antibody targeting SCF/c-kit signaling.

Kim, J.O.Kim, H.N.Kim, K.H.Baek, E.J.Park, J.Y.Ha, K.Heo, D.R.Seo, M.D.Park, S.G.

(2020) Int J Biol Macromol 159: 66-78

  • DOI: https://doi.org/10.1016/j.ijbiomac.2020.05.045
  • Primary Citation of Related Structures:  
    6LUN

  • PubMed Abstract: 

    CD117/c-kit, a tyrosine kinase receptor, plays a critical role in hematopoiesis, pigmentation, and fertility. The overexpression and activation of c-kit are thought to promote tumor growth and have been reported in various cancers, including leukemia, glioblastoma and mastocytosis. To disrupt the SCF/c-kit signaling axis in cancer, we generated a c-kit antagonist human antibody (NN2101) that binds to domain 2/3 of c-kit. This completely blocked the SCF-mediated phosphorylation of c-kit and inhibited TF-1 cell proliferation, erythroleukemia. In addition, the examination of binding affinity using surface plasmon resonance (SPR) assay showed that NN2101 can bind to c-kit of monkeys (K D  = 2.92 × 10 -10 M), rats (K D  = 1.68 × 10 -6 M), mice (K D  = 11.5 × 10 -9 M), and humans (K D  = 2.83 × 10 -12 M). We showed that NN2101 does not cause antibody-dependent cell-mediated cytotoxicity and complement-dependent cytotoxicity. The immunogenicity of NN2101 was similar to that of bevacizumab. Furthermore, the crystal structure of NN2101 Fab was determined and the structure of NN2101 Fab:c-kit complex was modeled. Structural information, as well as mutagenesis results, revealed that NN2101 can bind to the SCF-binding regions of c-kit. Collectively, we generated a c-kit neutralizing human antibody (NN2101) for the treatment of erythroleukemia and characterized its biophysical properties. NN2101 can potentially be used as a therapeutic antibody to treat different cancers.


  • Organizational Affiliation

    College of Pharmacy and Research Institute of Pharmaceutical Science and Technology (RIPST), Ajou University, 206 World Cup-ro, Yeongtong-gu, Suwon-si, Gyeonggi-do 16499, Republic of Korea.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
NN2101
A, C
218Homo sapiensMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
NN2101
B, D
218Homo sapiensMutation(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: 1.90 Å
  • R-Value Free: 0.210 
  • R-Value Work: 0.165 
  • R-Value Observed: 0.167 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 72.753α = 90
b = 69.702β = 107.71
c = 90.058γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data collection
PHENIXphasing
PHENIXmodel building
HKL-2000data scaling
HKL-2000data processing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2021-02-03
    Type: Initial release
  • Version 1.1: 2021-08-25
    Changes: Database references
  • Version 1.2: 2023-11-29
    Changes: Data collection, Refinement description