3HHA

Crystal structure of cathepsin L in complex with AZ12878478

• PDB DOI: https://doi.org/10.2210/pdb3HHA/pdb

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


• Deposited: 2009-05-15 Released: 2009-06-23 
• Deposition Author(s): Asaad, N., Bethel, P.A., Coulson, M.D., Dawson, J., Ford, S.J., Gerhardt, S., Grist, M., Hamlin, G.A., James, M.J., Jones, E.V., Karoutchi, G.I., Kenny, P.W., Morley, A.D., Oldham, K., Rankine, N., Ryan, D., Wells, S.L., Wood, L., Augustin, M., Krapp, S., Simader, H., Steinbacher, S.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.27 Å
• R-Value Free: 0.152 
• R-Value Work: 0.116 
• R-Value Observed: 0.118 

Literature

Dipeptidyl nitrile inhibitors of Cathepsin L.

Asaad, N., Bethel, P.A., Coulson, M.D., Dawson, J.E., Ford, S.J., Gerhardt, S., Grist, M., Hamlin, G.A., James, M.J., Jones, E.V., Karoutchi, G.I., Kenny, P.W., Morley, A.D., Oldham, K., Rankine, N., Ryan, D., Wells, S.L., Wood, L., Augustin, M., Krapp, S., Simader, H., Steinbacher, S.

(2009) Bioorg Med Chem Lett 19: 4280-4283

• PubMed: 19515558 
• DOI: https://doi.org/10.1016/j.bmcl.2009.05.071
• Primary Citation of Related Structures:  
  3HHA


• PubMed Abstract: 
  

  A series of potent Cathepsin L inhibitors with good selectivity with respect to other cysteine Cathepsins is described and SAR is discussed with reference to the crystal structure of a protein-ligand complex.

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Organizational Affiliation: 

Respiratory & Inflammation Research Area, 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: 98.68 kDa 
• Atom Count: 8,109 
• Modelled Residue Count: 869 
• Deposited Residue Count: 880 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Cathepsin L1	A, B, C, D	220	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 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NOW	E [auth A], H [auth B], J [auth C], K [auth D]	Nalpha-[(3-tert-butyl-1-methyl-1H-pyrazol-5-yl)carbonyl]-N-[(2Z)-2-iminoethyl]-3-methyl-L-phenylalaninamide C21 H29 N5 O2 TVOGNNSPACVESK-QPCOYWRUSA-N
PG4	F [auth A]	TETRAETHYLENE GLYCOL C8 H18 O5 UWHCKJMYHZGTIT-UHFFFAOYSA-N
PGE	I [auth B]	TRIETHYLENE GLYCOL C6 H14 O4 ZIBGPFATKBEMQZ-UHFFFAOYSA-N
GOL	L [auth D]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
ACT	G [auth A]	ACETATE ION C2 H3 O2 QTBSBXVTEAMEQO-UHFFFAOYSA-M

Binding Affinity Annotations
ID	Source	Binding Affinity
NOW	PDBBind:  3HHA	IC50: 12.6 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.27 Å
• R-Value Free: 0.152 
• R-Value Work: 0.116 
• R-Value Observed: 0.118 
• Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 57.26	α = 105.6
b = 62.69	β = 93.22
c = 68.24	γ = 115.55

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2009-06-23 
Deposition Author(s): Asaad, N., Bethel, P.A., Coulson, M.D., Dawson, J., Ford, S.J., Gerhardt, S., Grist, M., Hamlin, G.A., James, M.J., Jones, E.V., Karoutchi, G.I., Kenny, P.W., Morley, A.D., Oldham, K., Rankine, N., Ryan, D., Wells, S.L., Wood, L., Augustin, M., Krapp, S., Simader, H., Steinbacher, S.

Revision History  

• Version 1.0: 2009-06-23
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Non-polymer description, Version format compliance
• Version 1.2: 2018-05-30
  Changes: Advisory, Data collection, Derived calculations
• Version 1.3: 2021-10-13
  Changes: Database references, Derived calculations
• Version 1.4: 2024-10-16
  Changes: Data collection, Structure summary