5VEB

Crystal structure of a Fab binding to extracellular domain 5 of Cadherin-6


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.34 Å
  • R-Value Free: 0.252 
  • R-Value Work: 0.212 
  • R-Value Observed: 0.214 

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Ligand Structure Quality Assessment 


This is version 3.0 of the entry. See complete history


Literature

Discovery and Optimization of HKT288, a Cadherin-6-Targeting ADC for the Treatment of Ovarian and Renal Cancers.

Bialucha, C.U.Collins, S.D.Li, X.Saxena, P.Zhang, X.Durr, C.Lafont, B.Prieur, P.Shim, Y.Mosher, R.Lee, D.Ostrom, L.Hu, T.Bilic, S.Rajlic, I.L.Capka, V.Jiang, W.Wagner, J.P.Elliott, G.Veloso, A.Piel, J.C.Flaherty, M.M.Mansfield, K.G.Meseck, E.K.Rubic-Schneider, T.London, A.S.Tschantz, W.R.Kurz, M.Nguyen, D.Bourret, A.Meyer, M.J.Faris, J.E.Janatpour, M.J.Chan, V.W.Yoder, N.C.Catcott, K.C.McShea, M.A.Sun, X.Gao, H.Williams, J.Hofmann, F.Engelman, J.A.Ettenberg, S.A.Sellers, W.R.Lees, E.

(2017) Cancer Discov 7: 1030-1045

  • DOI: https://doi.org/10.1158/2159-8290.CD-16-1414
  • Primary Citation of Related Structures:  
    5VEB

  • PubMed Abstract: 

    Despite an improving therapeutic landscape, significant challenges remain in treating the majority of patients with advanced ovarian or renal cancer. We identified the cell-cell adhesion molecule cadherin-6 ( CDH6 ) as a lineage gene having significant differential expression in ovarian and kidney cancers. HKT288 is an optimized CDH6-targeting DM4-based antibody-drug conjugate (ADC) developed for the treatment of these diseases. Our study provides mechanistic evidence supporting the importance of linker choice for optimal antitumor activity and highlights CDH6 as an antigen for biotherapeutic development. To more robustly predict patient benefit of targeting CDH6, we incorporate a population-based patient-derived xenograft (PDX) clinical trial (PCT) to capture the heterogeneity of response across an unselected cohort of 30 models-a novel preclinical approach in ADC development. HKT288 induces durable tumor regressions of ovarian and renal cancer models in vivo , including 40% of models on the PCT, and features a preclinical safety profile supportive of progression toward clinical evaluation. Significance: We identify CDH6 as a target for biotherapeutics development and demonstrate how an integrated pharmacology strategy that incorporates mechanistic pharmacodynamics and toxicology studies provides a rich dataset for optimizing the therapeutic format. We highlight how a population-based PDX clinical trial and retrospective biomarker analysis can provide correlates of activity and response to guide initial patient selection for first-in-human trials of HKT288. Cancer Discov; 7(9); 1030-45. ©2017 AACR. This article is highlighted in the In This Issue feature, p. 920 .


  • Organizational Affiliation

    Novartis Institutes for Biomedical Research, Cambridge, Massachusetts. carl_uli.bialucha@novartis.com.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
anti-CDH6 Fab heavy chain225Homo sapiensMutation(s): 0 
UniProt
Find proteins for S6B291 (Homo sapiens)
Explore S6B291 
Go to UniProtKB:  S6B291
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupS6B291
Sequence Annotations
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
anti-CDH6 Fab light chainB,
D [auth L]
215Homo sapiensMutation(s): 0 
UniProt & NIH Common Fund Data Resources
Find proteins for P01834 (Homo sapiens)
Explore P01834 
Go to UniProtKB:  P01834
PHAROS:  P01834
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP01834
Sequence Annotations
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  • Reference Sequence
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
anti-CDH6 Fab heavy chainC [auth H]225Homo sapiensMutation(s): 0 
UniProt
Find proteins for S6B291 (Homo sapiens)
Explore S6B291 
Go to UniProtKB:  S6B291
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupS6B291
Sequence Annotations
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  • Reference Sequence
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Cadherin-6E [auth X],
F [auth Y]
125Homo sapiensMutation(s): 0 
Gene Names: CDH6
UniProt & NIH Common Fund Data Resources
Find proteins for P55285 (Homo sapiens)
Explore P55285 
Go to UniProtKB:  P55285
PHAROS:  P55285
GTEx:  ENSG00000113361 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP55285
Glycosylation
Glycosylation Sites: 2Go to GlyGen: P55285-1
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.34 Å
  • R-Value Free: 0.252 
  • R-Value Work: 0.212 
  • R-Value Observed: 0.214 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 78.829α = 90
b = 88.855β = 90
c = 186.73γ = 90
Software Package:
Software NamePurpose
XSCALEdata scaling
BUSTERrefinement
PDB_EXTRACTdata extraction
XDSdata reduction
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2017-06-07
    Type: Initial release
  • Version 1.1: 2017-09-13
    Changes: Database references
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Advisory, Atomic model, Data collection, Derived calculations, Structure summary
  • Version 3.0: 2024-04-24
    Changes: Atomic model, Data collection, Database references, Derived calculations, Non-polymer description, Polymer sequence, Source and taxonomy, Structure summary