1CVZ

CRYSTAL STRUCTURE ANALYSIS OF PAPAIN WITH CLIK148(CATHEPSIN L SPECIFIC INHIBITOR)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.70 Å
  • R-Value Free: 0.214 
  • R-Value Work: 0.177 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Inhibition mechanism of cathepsin L-specific inhibitors based on the crystal structure of papain-CLIK148 complex.

Tsuge, H.Nishimura, T.Tada, Y.Asao, T.Turk, D.Turk, V.Katunuma, N.

(1999) Biochem Biophys Res Commun 266: 411-416

  • DOI: 10.1006/bbrc.1999.1830
  • Primary Citation of Related Structures:  
    1CVZ

  • PubMed Abstract: 
  • Papain was used as an experimental model structure to understand the inhibition mechanism of newly developed specific inhibitors of cathepsin L, the papain superfamily. Recently, we developed a series of cathepsin L-specific inhibitors which are called the CLIK series [(1999) FEBS Lett ...

    Papain was used as an experimental model structure to understand the inhibition mechanism of newly developed specific inhibitors of cathepsin L, the papain superfamily. Recently, we developed a series of cathepsin L-specific inhibitors which are called the CLIK series [(1999) FEBS Lett. 458, 6-10]. Here, we report the complex structure of papain with CLIK148, which is a representative inhibitor from the CLIK series. The inhibitor complex structure was solved at 1.7 A resolution with conventional R 0.177. Unlike other epoxisuccinate inhibitors (E64, CA030, and CA074), CLIK148 uses both prime and nonprime sites, which are important for the specific inhibitory effect on cathepsin L. Also, the specificity for cathepsin L could be explained by the existence of Phe in the P2 site and hydrophobic interaction of N-terminal pyridine ring.


    Organizational Affiliation

    Institute for Health Sciences, Tokushima Bunri University, Yamashiro-cho, Tokushima, 770-8514, Japan. tsuge@tokushima.bunri-u.ac.jp



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
PAPAINA212Carica papayaMutation(s): 0 
EC: 3.4.22.2
UniProt
Find proteins for P00784 (Carica papaya)
Explore P00784 
Go to UniProtKB:  P00784
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP00784
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
C48
Query on C48

Download Ideal Coordinates CCD File 
B [auth A]N1-(1-DIMETHYLCARBAMOYL-2-PHENYL-ETHYL)-2-OXO-N4-(2-PYRIDIN-2-YL-ETHYL)-SUCCINAMIDE
C22 H26 N4 O4
ZPFPZRVOBBMZMP-SFHVURJKSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.70 Å
  • R-Value Free: 0.214 
  • R-Value Work: 0.177 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 42.89α = 90
b = 49.91β = 90
c = 95.76γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
X-PLORrefinement

Structure Validation

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Entry History 

Deposition Data

  • Released Date: 2000-08-30 
  • Deposition Author(s): Tsuge, H.

Revision History  (Full details and data files)

  • Version 1.0: 2000-08-30
    Type: Initial release
  • Version 1.1: 2008-04-27
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance