4K94

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free: 0.235 
  • R-Value Work: 0.198 
  • R-Value Observed: 0.200 

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This is version 1.3 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 U S A 110: 17832-17837

  • DOI: https://doi.org/10.1073/pnas.1317118110
  • Primary Citation of Related Structures:  
    4K94, 4K9E

  • 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 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
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Fab19 heavy chainA [auth L]226Homo sapiensMutation(s): 0 
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Fab19 light chainB [auth H]220Homo sapiensMutation(s): 0 
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Mast/stem cell growth factor receptor Kit214Homo sapiensMutation(s): 0 
Gene Names: KITSCFR
EC: 2.7.10.1
UniProt & NIH Common Fund Data Resources
Find proteins for P10721 (Homo sapiens)
Explore P10721 
Go to UniProtKB:  P10721
GTEx:  ENSG00000157404 
Entity Groups  
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UniProt GroupP10721
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
NAG
Query on NAG

Download Ideal Coordinates CCD File 
D [auth C]2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
Experimental Data & Validation

Experimental Data

Unit Cell:
Length ( Å )Angle ( ˚ )
a = 169.58α = 90
b = 48.98β = 122.38
c = 106.97γ = 90
Software Package:
Software NamePurpose
CBASSdata collection
PHASERphasing
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2013-10-16
    Type: Initial release
  • Version 1.1: 2014-03-12
    Changes: Database references
  • Version 1.2: 2014-04-09
    Changes: Source and taxonomy
  • Version 1.3: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Data collection, Database references, Derived calculations, Structure summary