6AY2 | pdb_00006ay2

Structure of CathB with covalently linked Compound 28


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.60 Å
  • R-Value Free: 
    0.176 (Depositor), 0.190 (DCC) 
  • R-Value Work: 
    0.161 (Depositor), 0.178 (DCC) 
  • R-Value Observed: 
    0.162 (Depositor) 

wwPDB Validation 3D Report Full Report

Validation slider image for 6AY2

Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history

Literature

Discovery of Peptidomimetic Antibody-Drug Conjugate Linkers with Enhanced Protease Specificity.

Wei, B.Gunzner-Toste, J.Yao, H.Wang, T.Wang, J.Xu, Z.Chen, J.Wai, J.Nonomiya, J.Tsai, S.P.Chuh, J.Kozak, K.R.Liu, Y.Yu, S.F.Lau, J.Li, G.Phillips, G.D.Leipold, D.Kamath, A.Su, D.Xu, K.Eigenbrot, C.Steinbacher, S.Ohri, R.Raab, H.Staben, L.R.Zhao, G.Flygare, J.A.Pillow, T.H.Verma, V.Masterson, L.A.Howard, P.W.Safina, B.

(2018) J Med Chem 61: 989-1000

  • DOI: https://doi.org/10.1021/acs.jmedchem.7b01430
  • Primary Citation Related Structures: 
    6AY2

  • PubMed Abstract: 

    Antibody-drug conjugates (ADCs) have become an important therapeutic modality for oncology, with three approved by the FDA and over 60 others in clinical trials. Despite the progress, improvements in ADC therapeutic index are desired. Peptide-based ADC linkers that are cleaved by lysosomal proteases have shown sufficient stability in serum and effective payload-release in targeted cells. If the linker can be preferentially hydrolyzed by tumor-specific proteases, safety margin may improve. However, the use of peptide-based linkers limits our ability to modulate protease specificity. Here we report the structure-guided discovery of novel, nonpeptidic ADC linkers. We show that a cyclobutane-1,1-dicarboxamide-containing linker is hydrolyzed predominantly by cathepsin B while the valine-citrulline dipeptide linker is not. ADCs bearing the nonpeptidic linker are as efficacious and stable in vivo as those with the dipeptide linker. Our results strongly support the application of the peptidomimetic linker and present new opportunities for improving the selectivity of ADCs.


  • Organizational Affiliation
    • Genentech, Inc. , 1 DNA Way, South San Francisco, California 94080, United States.

Macromolecule Content 

  • Total Structure Weight: 56.74 kDa 
  • Atom Count: 4,202 
  • Modeled Residue Count: 509 
  • Deposited Residue Count: 510 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Cathepsin B
A, B
255Homo sapiensMutation(s): 0 
Gene Names: CTSBCPSB
EC: 3.4.22.1
UniProt & NIH Common Fund Data Resources
Find proteins for P07858 (Homo sapiens)
Explore P07858 
Go to UniProtKB:  P07858
PHAROS:  P07858
GTEx:  ENSG00000164733 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP07858
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
C1G
(Subject of Investigation/LOI)

Query on C1G



Download:Ideal Coordinates CCD File
C [auth A],
D [auth B]
N~1~-[(2S)-1-amino-5-(carbamoylamino)pentan-2-yl]-N'~1~-[(1R)-1-(thiophen-3-yl)ethyl]cyclobutane-1,1-dicarboxamide
C18 H29 N5 O3 S
QWGHBARYVOPELP-OCCSQVGLSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.60 Å
  • R-Value Free:  0.176 (Depositor), 0.190 (DCC) 
  • R-Value Work:  0.161 (Depositor), 0.178 (DCC) 
  • R-Value Observed: 0.162 (Depositor) 
Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 31.317α = 90
b = 127.243β = 102.9
c = 70.034γ = 90
Software Package:
Software NamePurpose
XSCALEdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
XDSdata reduction
PHASERphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2017-12-27
    Type: Initial release
  • Version 1.1: 2018-02-21
    Changes: Database references
  • Version 1.2: 2024-10-16
    Changes: Advisory, Data collection, Database references, Structure summary