1FH0 | pdb_00001fh0

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

• PDB DOI: https://doi.org/10.2210/pdb1FH0/pdb

• Classification: HYDROLASE/HYDROLASE inhibitor
• Organism(s): Homo sapiens
• Expression System: Saccharomyces cerevisiae
• Mutation(s): Yes 


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

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.60 Å
• R-Value Free: 
  0.211 (Depositor) 
• R-Value Work: 
  0.197 (Depositor) 
• R-Value Observed: 
  0.198 (Depositor) 

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: 11027133 
• DOI: https://doi.org/10.1021/bi000951p
• Primary Citation Related Structures: 
  1FH0


• 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 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. [e-mail]

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 49.33 kDa 
• Atom Count: 3,757 
• Modeled Residue Count: 442 
• Deposited Residue Count: 442 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
CATHEPSIN V	A, B	221	Homo sapiens	Mutation(s): 2  EC: 3.4.22 (PDB Primary Data), 3.4.22.43 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for O60911 (Homo sapiens) Explore O60911  Go to UniProtKB:  O60911
PHAROS:  O60911 GTEx:  ENSG00000136943

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
0IW	C [auth A], E [auth B]	Nalpha-[(4-methylpiperazin-1-yl)carbonyl]-N-[(3S)-1-phenyl-5-(phenylsulfonyl)pentan-3-yl]-L-phenylalaninamide C32 H40 N4 O4 S VZSXPUDQSLKVIR-JDXGNMNLSA-N
SO4	D [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Biologically Interesting Molecules (External Reference) 

1 Unique

Entity ID: 2
ID	Chains	Name	Type/Class	2D Diagram	3D Interactions
PRD_000325 (0IW)	C [auth A], E [auth B]	MePip-Phe-HphVSPh	Peptide-like / Inhibitor

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.60 Å
• R-Value Free:  0.211 (Depositor) 
• R-Value Work:  0.197 (Depositor) 
• R-Value Observed: 0.198 (Depositor) 

Space Group: P 6₄ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 104.7	α = 90
b = 104.7	β = 90
c = 179.2	γ = 120

Software Package:

Software Name	Purpose
MAR345	data collection
DENZO	data reduction
SCALEPACK	data scaling
EPMR	phasing
CNX	refinement

Structure Validation

Entry History 

Deposition Data

• 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
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Atomic model, Database references, Derived calculations, Non-polymer description, Structure summary, Version format compliance
• Version 1.3: 2011-10-12
  Changes: Non-polymer description
• Version 1.4: 2013-02-27
  Changes: Other
• Version 1.5: 2017-10-04
  Changes: Refinement description
• Version 1.6: 2021-11-03
  Changes: Database references, Derived calculations
• Version 1.7: 2024-03-13
  Changes: Data collection, Source and taxonomy, Structure summary
• Version 1.8: 2024-11-20
  Changes: Structure summary