8B4T | pdb_00008b4t

Human cathepsin B in complex with the carbamate inhibitor 7


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.45 Å
  • R-Value Free: 
    0.208 (Depositor), 0.220 (DCC) 
  • R-Value Work: 
    0.177 (Depositor), 0.180 (DCC) 
  • R-Value Observed: 
    0.179 (Depositor) 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history


Literature

Redirecting the Peptide Cleavage Causes Protease Inactivation.

Breuer, C.Kuppers, J.Schulz-Fincke, A.C.Heilos, A.Lemke, C.Spiwokova, P.Schmitz, J.Cremer, L.Frigole-Vivas, M.Lulsdorff, M.Mertens, M.D.Wichterle, F.Apeltauer, M.Horn, M.Gilberg, E.Furtmann, N.Bajorath, J.Bartz, U.Engels, B.Mares, M.Gutschow, M.

(2025) Angew Chem Int Ed Engl 64: e202506832-e202506832

  • DOI: https://doi.org/10.1002/anie.202506832
  • Primary Citation of Related Structures:  
    8B4T, 8B5F

  • PubMed Abstract: 

    Cysteine and serine proteases cleave peptides through covalent catalysis by generating a transient adduct with the N-terminal part of the substrate after releasing its C-terminal part. We demonstrate the unique redirection of this event leading to strong enzyme inactivation. For targeting human cathepsin B, a cysteine protease of significant therapeutic importance, we designed tailored peptidomimetics with a variety of dipeptide fragments directed toward the occluding loop and equipped with numerous N-terminal carbamate warheads. The carbamate deprotonation catalyzed by the active site thiolate initiates the redirected cleavage. The C-terminal part of the inhibitors remains covalently attached to the protease. Hydrolysis of such carbamoyl-enzyme complexes is catalytically unsupported rendering inhibition irreversible. This novel mechanism of action comprises a significant extension of the covalent drug space.


  • Organizational Affiliation
    • Pharmaceutical Institute, Pharmaceutical & Medicinal Chemistry, University of Bonn, An der Immenburg 4, 53121, Bonn, Germany.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Cathepsin B255Homo sapiensMutation(s): 1 
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
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
P9F (Subject of Investigation/LOI)
Query on P9F

Download Ideal Coordinates CCD File 
B [auth A](2S)-2-[[(2S)-2-[(4-chloranylphenoxy)carbonylamino]-3-cyclohexyl-propanoyl]amino]-3-phenyl-propanoic acid
C25 H29 Cl N2 O5
XQAHEQBJBQAMLZ-VXKWHMMOSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.45 Å
  • R-Value Free:  0.208 (Depositor), 0.220 (DCC) 
  • R-Value Work:  0.177 (Depositor), 0.180 (DCC) 
  • R-Value Observed: 0.179 (Depositor) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 30.75α = 90
b = 81.55β = 90
c = 93.46γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
XSCALEdata scaling
MOLREPphasing
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Ministry of Education, Youth and Sports of the Czech RepublicCzech Republic--
European Regional Development FundEuropean Union--

Revision History  (Full details and data files)

  • Version 1.0: 2023-10-04
    Type: Initial release
  • Version 1.1: 2024-11-20
    Changes: Structure summary
  • Version 1.2: 2025-08-27
    Changes: Database references