Crystal Structure Analysis of Bovine Spleen Cathepsin B-E64c complex

Experimental Data Snapshot

  • Resolution: 2.29 Å
  • R-Value Free: 0.239 
  • R-Value Work: 0.197 

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Structural basis for development of cathepsin B-specific noncovalent-type inhibitor: crystal structure of cathepsin B-E64c complex

Yamamoto, A.Tomoo, T.Matsugi, K.Hara, T.In, Y.Murata, M.Kitamura, K.Ishida, T.

(2002) Biochim Biophys Acta 1597: 244-251

  • DOI: https://doi.org/10.1016/s0167-4838(02)00284-4
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    In order to elucidate the substrate specificity of the Sn subsites (n=1-3) of cathepsin B, its crystal structure inhibited by E64c [(+)-(2S,3S)-3-(1-[N-(3-methylbutyl)amino]-leucylcarbonyl)oxirane-2-carboxylic acid] was analyzed by the X-ray diffraction method. Iterative manual rebuilding and convenient conjugate refinement of structure decreased R- and free R-factors to 19.7% and to 23.9%, respectively, where 130 water molecules were included for the refinement using 14,759 independent reflections from 10 to 2.3 A resolution. The epoxy carbonyl carbon of E64c was covalently bonded to the Cys(29) S(gamma) atom and the remaining parts were located at Sn subsites (n=1-3). The substrate specificity of these subsites was characterized based on their interactions with the inhibitor. Base on these structural data, we developed a novel cathepsin B-specific noncovalent-type inhibitor, which may bind to S2'-S3. The molecular design of possessing structural elements of both CA074 and E64c, assisted by energy minimization and molecular dynamics (MD) simulation, may lead to a new lead noncovalent-type inhibitor.

  • Organizational Affiliation

    Department of Physical Chemistry, Osaka University of Pharmaceutical Sciences, 4-20-1 Nasahara, Takatsuki, Osaka 569-1094, Japan.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Cathepsin B256Bos taurusMutation(s): 0 
Find proteins for P07688 (Bos taurus)
Explore P07688 
Go to UniProtKB:  P07688
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP07688
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on E6C

Download Ideal Coordinates CCD File 
C15 H28 N2 O5
Experimental Data & Validation

Experimental Data

  • Resolution: 2.29 Å
  • R-Value Free: 0.239 
  • R-Value Work: 0.197 
  • Space Group: P 43 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 72.578α = 90
b = 72.578β = 90
c = 141.835γ = 90
Software Package:
Software NamePurpose

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2003-01-19
    Type: Initial release
  • Version 1.1: 2008-04-27
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2017-10-04
    Changes: Refinement description
  • Version 1.4: 2023-10-25
    Changes: Data collection, Database references, Derived calculations, Refinement description