4K94

Crystal structure of KIT D4D5 fragment in complex with anti-Kit antibody Fab19


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.4 Å
  • R-Value Free: 0.235 
  • R-Value Work: 0.198 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Structural basis for KIT receptor tyrosine kinase inhibition by antibodies targeting the D4 membrane-proximal region.

Reshetnyak, A.V.Nelson, B.Shi, X.Boggon, T.J.Pavlenco, A.Mandel-Bausch, E.M.Tome, F.Suzuki, Y.Sidhu, S.S.Lax, I.Schlessinger, J.

(2013) Proc.Natl.Acad.Sci.USA 110: 17832-17837

  • DOI: 10.1073/pnas.1317118110
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Somatic oncogenic mutations in the receptor tyrosine kinase KIT function as major drivers of gastrointestinal stromal tumors and a subset of acute myeloid leukemia, melanoma, and other cancers. Although treatment of these cancers with tyrosine kinase ...

    Somatic oncogenic mutations in the receptor tyrosine kinase KIT function as major drivers of gastrointestinal stromal tumors and a subset of acute myeloid leukemia, melanoma, and other cancers. Although treatment of these cancers with tyrosine kinase inhibitors shows dramatic responses and durable disease control, drug resistance followed by clinical progression of disease eventually occurs in virtually all patients. In this report, we describe inhibitory KIT antibodies that bind to the membrane-proximal Ig-like D4 of KIT with significant overlap with an epitope in D4 that mediates homotypic interactions essential for KIT activation. Crystal structures of the anti-KIT antibody in complex with KIT D4 and D5 allowed design of affinity-matured libraries that were used to isolate variants with increased affinity and efficacy. Isolated antibodies showed KIT inhibition together with suppression of cell proliferation driven by ligand-stimulated WT or constitutively activated oncogenic KIT mutant. These antibodies represent a unique therapeutic approach and a step toward the development of "naked" or toxin-conjugated KIT antibodies for the treatment of KIT-driven cancers.


    Organizational Affiliation

    Department of Pharmacology, Yale University School of Medicine, New Haven, CT 06520.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Fab19 heavy chain
L
226N/A
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Fab19 light chain
H
220N/A
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
Mast/stem cell growth factor receptor Kit
C
214Homo sapiensGene Names: KIT (SCFR)
EC: 2.7.10.1
Find proteins for P10721 (Homo sapiens)
Go to Gene View: KIT
Go to UniProtKB:  P10721
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NAG
Query on NAG

Download SDF File 
Download CCD File 
C
N-ACETYL-D-GLUCOSAMINE
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.4 Å
  • R-Value Free: 0.235 
  • R-Value Work: 0.198 
  • Space Group: C 1 2 1
  • Diffraction Data DOI: 
    10.15785/SBGRID/164 SBGrid
Unit Cell:
Length (Å)Angle (°)
a = 169.580α = 90.00
b = 48.980β = 122.38
c = 106.970γ = 90.00
Software Package:
Software NamePurpose
PHENIXrefinement
PHASERphasing
HKL-2000data reduction
HKL-2000data scaling
CBASSdata collection

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2013-10-16
    Type: Initial release
  • Version 1.1: 2014-03-12
    Type: Database references
  • Version 1.2: 2014-04-09
    Type: Source and taxonomy