1M6D

Crystal structure of human cathepsin F


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.70 Å
  • R-Value Free: 0.222 
  • R-Value Work: 0.195 
  • R-Value Observed: 0.198 

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Ligand Structure Quality Assessment 


This is version 1.5 of the entry. See complete history


Literature

The crystal structure of human cathepsin F and its implications for the development of novel immunomodulators

Somoza, J.R.Palmer, J.T.Ho, J.D.

(2002) J Mol Biol 322: 559-568

  • DOI: https://doi.org/10.1016/s0022-2836(02)00780-5
  • Primary Citation of Related Structures:  
    1M6D

  • PubMed Abstract: 

    Cathepsin F is a lysosomal cysteine protease of the papain family, and likely plays a regulatory role in processing the invariant chain that is associated with the major histocompatibility complex (MHC) class II. Evidence suggests that inhibiting cathepsin F activity will block MHC class II processing in macrophages. Consequently, inhibitors of this enzyme may be useful in treating certain diseases that involve an inappropriate or excessive immune response. We have determined the 1.7A structure of the mature domain of human cathepsin F associated with an irreversible vinyl sulfone inhibitor. This structure provides a basis for understanding cathepsin F's substrate specificity, and suggests ways of identifying potent and selective inhibitors of this enzyme.


  • Organizational Affiliation

    Department of Medicinal and Structural Chemistry, Celera, 180 Kimball Way, 94080, South San Francisco, CA, USA. john.somoza@elera.com


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Cathepsin F
A, B
214Homo sapiensMutation(s): 3 
Gene Names: CATF
EC: 3.4.22.41
UniProt & NIH Common Fund Data Resources
Find proteins for Q9UBX1 (Homo sapiens)
Explore Q9UBX1 
Go to UniProtKB:  Q9UBX1
PHAROS:  Q9UBX1
GTEx:  ENSG00000174080 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9UBX1
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
MYP
Query on MYP

Download Ideal Coordinates CCD File 
C [auth A],
D [auth B]
4-MORPHOLIN-4-YL-PIPERIDINE-1-CARBOXYLIC ACID [1-(3-BENZENESULFONYL-1-PROPYL-ALLYLCARBAMOYL)-2-PHENYLETHYL]-AMIDE
C31 H42 N4 O5 S
OFBHNKJTHNHXQT-WNJJXGMVSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.70 Å
  • R-Value Free: 0.222 
  • R-Value Work: 0.195 
  • R-Value Observed: 0.198 
  • Space Group: P 21 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 68.25α = 90
b = 103.26β = 90
c = 58.65γ = 90
Software Package:
Software NamePurpose
MAR345data collection
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
CNXrefinement

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2003-07-15
    Type: Initial release
  • Version 1.1: 2008-04-28
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2013-07-17
    Changes: Non-polymer description
  • Version 1.4: 2017-10-11
    Changes: Refinement description
  • Version 1.5: 2021-10-27
    Changes: Database references, Derived calculations