3HWN | pdb_00003hwn

CATHEPSIN L with AZ13010160

• PDB DOI: https://doi.org/10.2210/pdb3HWN/pdb

• Classification: HYDROLASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2009-06-18 Released: 2009-09-15 
• Deposition Author(s): Kenny, P., Morley, A.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.33 Å
• R-Value Free: 
  0.347 (Depositor), 0.358 (DCC) 
• R-Value Work: 
  0.250 (Depositor), 0.258 (DCC) 
• R-Value Observed: 
  0.252 (Depositor) 

Literature

Design of selective Cathepsin inhibitors

Bethel, P.A., Gerhardt, S., Jones, E.V., Kenny, P.W., Karoutchi, G.I., Morley, A.D., Oldham, K., Rankine, N., Augustin, M., Krapp, S., Simader, H., Steinbacher, S.

(2009) Bioorg Med Chem Lett 19: 4622-4625

• PubMed: 19616430 
• DOI: https://doi.org/10.1016/j.bmcl.2009.06.090
• Primary Citation Related Structures: 
  3HWN


• PubMed Abstract: 
  

  A number of molecular recognition features have been exploited in structure-based design of selective Cathepsin inhibitors.

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Organizational Affiliation: 
• RIRA, AstraZeneca, Mereside, Alderley Park, Macclesfield SK10 4TG, UK.

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)

Biological Assembly 3  

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

Biological assembly 3 assigned by authors and generated by PISA (software)

Biological Assembly 4  

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

Biological assembly 4 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 116.57 kDa 
• Atom Count: 6,934 
• Modeled Residue Count: 862 
• Deposited Residue Count: 1,032 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Cathepsin L1	A, B, C, D	258	Homo sapiens	Mutation(s): 1  Gene Names: CTSL1, CTSL EC: 3.4.22.15
UniProt & NIH Common Fund Data Resources
Find proteins for P07711 (Homo sapiens) Explore P07711  Go to UniProtKB:  P07711
PHAROS:  P07711 GTEx:  ENSG00000135047

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
BD3	E [auth A], F [auth B], G [auth C], H [auth D]	Nalpha-[(3-tert-butyl-1-methyl-1H-pyrazol-5-yl)carbonyl]-N-[(2E)-2-iminoethyl]-3-{5-[(Z)-iminomethyl]-1,3,4-oxadiazol-2-yl}-L-phenylalaninamide C23 H28 N8 O3 TVWDSIGUOHNHHP-TTWIPJPDSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.33 Å
• R-Value Free:  0.347 (Depositor), 0.358 (DCC) 
• R-Value Work:  0.250 (Depositor), 0.258 (DCC) 
• R-Value Observed: 0.252 (Depositor) 

Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 57.07	α = 105.34
b = 62.8	β = 94.04
c = 67.97	γ = 115.26

Software Package:

Software Name	Purpose
MOLREP	phasing
REFMAC	refinement
XDS	data reduction
XSCALE	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2009-09-15 
Deposition Author(s): Kenny, P., Morley, A.

Revision History  

• Version 1.0: 2009-09-15
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2017-11-01
  Changes: Advisory, Refinement description
• Version 1.3: 2021-10-13
  Changes: Advisory, Database references, Derived calculations
• Version 1.4: 2024-11-06
  Changes: Data collection, Structure summary