2DC9

X-ray crystal structure analysis of bovine spleen cathepsin B-CA074Me complex

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.94 Å
  • R-Value Free: 0.221 
  • R-Value Work: 0.190 
  • R-Value Observed: 0.190 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 1.4 of the entry. See complete history. 


Literature

Quantitative estimation of each active subsite of cathepsin B for the inhibitory activity, based on the inhibitory activitybinding mode relationship of a series of epoxysuccinyl inhibitors by X-ray crystal structure analyses of the complexes

Watanabe, D., Yamamoto, A., Matsumoto, K., Murata, M., Kitamura, K., Tomoo, K., Ishida, T.

To be published.

Macromolecules
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(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
CATHEPSIN B256Bos taurusMutation(s): 0 
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
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
74M
Query on 74M
Download Ideal Coordinates CCD File 
C [auth A]METHYL N-({(2S,3S)-3-[(PROPYLAMINO)CARBONYL]OXIRAN-2-YL}CARBONYL)-L-ISOLEUCYL-L-PROLINATE
C19 H31 N3 O6
XGWSRLSPWIEMLQ-YTFOTSKYSA-N
PO4
Query on PO4
Download Ideal Coordinates CCD File 
B [auth A]PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
GOL
Query on GOL
Download Ideal Coordinates CCD File 
D [auth A]GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
Binding Affinity Annotations 
IDSourceBinding Affinity
74M BindingDB:  2DC9 IC50: min: 80, max: 6.80e+4 (nM) from 2 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.94 Å
  • R-Value Free: 0.221 
  • R-Value Work: 0.190 
  • R-Value Observed: 0.190 
  • Space Group: P 43 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 72.32α = 90
b = 72.32β = 90
c = 139.69γ = 90
Software Package:
Software NamePurpose
CNSrefinement
CNSphasing

Structure Validation

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Ligand Structure Quality Assessment 


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Entry History 

Deposition Data

  • Released Date: 2006-01-24 
    • Deposition Author(s): Watanabe, D.

Revision History  (Full details and data files)

  • Version 1.0: 2006-01-24
    Type: Initial release
  • Version 1.1: 2008-04-30
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Non-polymer description, Version format compliance
  • Version 1.3: 2017-10-11
    Changes: Refinement description
  • Version 1.4: 2023-10-25
    Changes: Data collection, Database references, Derived calculations, Refinement description, Structure summary