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: 2.2 Å
  • R-Value Work: 0.194 

wwPDB Validation 3D Report Full Report


This is version 1.5 of the entry. See complete history. 

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

  • 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 ...

    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

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Cathepsin B
A
48Bos taurusMutation(s): 0 
Gene Names: CTSB
EC: 3.4.22.1
Find proteins for P07688 (Bos taurus)
Go to Gene View: CTSB
Go to UniProtKB:  P07688
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Cathepsin B
B
205Bos taurusMutation(s): 0 
Gene Names: CTSB
EC: 3.4.22.1
Find proteins for P07688 (Bos taurus)
Go to Gene View: CTSB
Go to UniProtKB:  P07688
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
EP2
Query on EP2
Download SDF File 
Download CCD File 
B
methyl N-[(2S)-4-{[(1S)-1-{[(2S)-2-carboxypyrrolidin-1-yl]carbonyl}-3-methylbutyl]amino}-2-hydroxy-4-oxobutanoyl]-L-leucylglycylglycinate
NS-134
C26 H41 N5 O10
LLLKOFOBLVPXQZ-RNEDXHKXSA-N
 Ligand Interaction
Biologically Interesting Molecules 1 Unique
IDChainsNameType/Class2D Diagram3D Interactions
PRD_000444 (EP2)
Query on PRD_000444		BNS-134 TWO HEADED EPOXYSUCCINYL INHIBITORPeptide-like / Inhibitor

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Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.2 Å
  • R-Value Work: 0.194 
  • Space Group: P 43 21 2
Unit Cell:
Length (Å)Angle (°)
a = 73.064α = 90.00
b = 73.064β = 90.00
c = 141.970γ = 90.00
Software Package:
Software NamePurpose
MAINrefinement
SCALEPACKdata scaling
EPMRphasing
DENZOdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots


View more in-depth experimental data

Entry History 

Deposition Data

Revision History 

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