1FH0

CRYSTAL STRUCTURE OF HUMAN CATHEPSIN V COMPLEXED WITH AN IRREVERSIBLE VINYL SULFONE INHIBITOR


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.6 Å
  • R-Value Free: 0.211 
  • R-Value Work: 0.197 

wwPDB Validation 3D Report Full Report


This is version 1.5 of the entry. See complete history

Literature

Crystal structure of human cathepsin V.

Somoza, J.R.Zhan, H.Bowman, K.K.Yu, L.Mortara, K.D.Palmer, J.T.Clark, J.M.McGrath, M.E.

(2000) Biochemistry 39: 12543-12551


  • PubMed Abstract: 
  • Cathepsin V is a lysosomal cysteine protease that is expressed in the thymus, testis and corneal epithelium. We have determined the 1.6 A resolution crystal structure of human cathepsin V associated with an irreversible vinyl sulfone inhibitor. The f ...

    Cathepsin V is a lysosomal cysteine protease that is expressed in the thymus, testis and corneal epithelium. We have determined the 1.6 A resolution crystal structure of human cathepsin V associated with an irreversible vinyl sulfone inhibitor. The fold of this enzyme is similar to the fold adopted by other members of the papain superfamily of cysteine proteases. This study provides a framework for understanding the structural basis for cathepsin V's activity and will aid in the design of inhibitors of this enzyme. A comparison of cathepsin V's active site with the active sites of related proteases revealed a number of differences, especially in the S2 and S3 subsites, that could be exploited in identifying specific cathepsin V inhibitors or in identifying inhibitors of other cysteine proteases that would be selective against cathepsin V.


    Organizational Affiliation

    Axys Pharmaceuticals, Inc., 385 Oyster Point Boulevard, Suite 1, South San Francisco, California 94080, USA. john_somoza@axyspharm.com




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
CATHEPSIN V
A, B
221Homo sapiensMutation(s): 2 
Gene Names: CTSV (CATL2, CTSL2, CTSU)
EC: 3.4.22.43
Find proteins for O60911 (Homo sapiens)
Go to Gene View: CTSV
Go to UniProtKB:  O60911
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download SDF File 
Download CCD File 
A
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
0IW
Query on 0IW

Download SDF File 
Download CCD File 
A, B
Nalpha-[(4-methylpiperazin-1-yl)carbonyl]-N-[(3S)-1-phenyl-5-(phenylsulfonyl)pentan-3-yl]-L-phenylalaninamide
APC-3316, bound form; 4-Methylpiperazine-1-carboxylic acid [1-[(3-benzenesulfonyl-1-phenethylallyl)carbamoyl]-2-phenylethyl]amide, bound form
C32 H40 N4 O4 S
VZSXPUDQSLKVIR-JDXGNMNLSA-N
 Ligand Interaction
Biologically Interesting Molecules 1 Unique
IDChainsNameType/Class2D Diagram3D Interactions
PRD_000325 (0IW)
Query on PRD_000325
A,BMePip-Phe-HphVSPhPeptide-like / Inhibitor

--

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.6 Å
  • R-Value Free: 0.211 
  • R-Value Work: 0.197 
  • Space Group: P 64 2 2
Unit Cell:
Length (Å)Angle (°)
a = 104.700α = 90.00
b = 104.700β = 90.00
c = 179.200γ = 120.00
Software Package:
Software NamePurpose
MAR345data collection
CNXrefinement
DENZOdata reduction
EPMRphasing
SCALEPACKdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 2000-07-30 
  • Released Date: 2001-07-30 
  • Deposition Author(s): Somoza, J.R.

Revision History 

  • Version 1.0: 2001-07-30
    Type: Initial release
  • Version 1.1: 2008-04-27
    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: 2011-10-12
    Type: Non-polymer description
  • Version 1.4: 2013-02-27
    Type: Other
  • Version 1.5: 2017-10-04
    Type: Refinement description