1SP4

Crystal structure of NS-134 in complex with bovine cathepsin B: a two headed epoxysuccinyl inhibitor extends along the whole active site cleft

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Work: 0.194 

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Literature

Crystal structure of NS-134 in complex with bovine cathepsin B: a two-headed epoxysuccinyl inhibitor extends along the entire active-site cleft.

Stern, I., Schaschke, N., Moroder, L., Turk, D.

(2004) Biochem J 381: 511-517

  • DOI: 10.1042/BJ20040237
  • Primary Citation of Related Structures:  
    1SP4

  • PubMed Abstract: 

    • The crystal structure of the inhibitor NS-134 in complex with bovine cathepsin B reveals that functional groups attached to both sides of the epoxysuccinyl reactive group bind to the part of active-site cleft as predicted. The -Leu-Pro-OH side binds to the primed binding sites interacting with the His110 and His111 residues with its C-terminal carboxy group, whereas the -Leu-Gly-Meu (-Leu-Gly-Gly-OMe) part (Meu, methoxycarbonylmethyl) binds along the non-primed binding sites ...

    The crystal structure of the inhibitor NS-134 in complex with bovine cathepsin B reveals that functional groups attached to both sides of the epoxysuccinyl reactive group bind to the part of active-site cleft as predicted. The -Leu-Pro-OH side binds to the primed binding sites interacting with the His110 and His111 residues with its C-terminal carboxy group, whereas the -Leu-Gly-Meu (-Leu-Gly-Gly-OMe) part (Meu, methoxycarbonylmethyl) binds along the non-primed binding sites. Comparison with the propeptide structures of cathepsins revealed that the binding of the latter part is least similar to the procathepsin B structure; this result, together with the two-residue shift in positioning of the Leu-Gly-Gly part, suggests that the propeptide structures of the cognate enzymes may not be the best starting point for the design of reverse binding inhibitors.

    Organizational Affiliation: 

    Department of Biochemistry and Molecular Biology, Josef Stefan Institute, Jamova 39, SI-1000 Ljubljana, Slovenia.



Macromolecules
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Cathepsin BA48Bos taurusMutation(s): 0 
Gene Names: CTSB
EC: 3.4.22.1
UniProt
Find proteins for P07688 (Bos taurus)
Explore P07688 
Go to UniProtKB:  P07688
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP07688
Protein Feature View
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  • Reference Sequence
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(by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Cathepsin BB205Bos taurusMutation(s): 0 
Gene Names: CTSB
EC: 3.4.22.1
UniProt
Find proteins for P07688 (Bos taurus)
Explore P07688 
Go to UniProtKB:  P07688
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP07688
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
EP2
Query on EP2
Download Ideal Coordinates CCD File 
C [auth B]methyl N-[(2S)-4-{[(1S)-1-{[(2S)-2-carboxypyrrolidin-1-yl]carbonyl}-3-methylbutyl]amino}-2-hydroxy-4-oxobutanoyl]-L-leucylglycylglycinate
C26 H41 N5 O10
LLLKOFOBLVPXQZ-RNEDXHKXSA-N		 Ligand Interaction
Biologically Interesting Molecules (External Reference) 1 Unique
Entity ID: 3
IDChainsNameType/Class2D Diagram3D Interactions
PRD_000444 (EP2)
Query on PRD_000444		C [auth B]NS-134 TWO HEADED EPOXYSUCCINYL INHIBITORPeptide-like / Inhibitor Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Work: 0.194 
  • Space Group: P 43 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 73.064α = 90
b = 73.064β = 90
c = 141.97γ = 90
Software Package:
Software NamePurpose
MAINrefinement
DENZOdata reduction
SCALEPACKdata scaling
EPMRphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2004-05-04
    Type: Initial release
  • Version 1.1: 2008-04-29
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Atomic model, Database references, Derived calculations, Non-polymer description, Structure summary, Version format compliance
  • Version 1.3: 2012-12-12
    Changes: Other
  • Version 1.4: 2014-02-12
    Changes: Refinement description
  • Version 1.5: 2017-10-11
    Changes: Advisory, Refinement description