Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

Global Symmetry: Cyclic - C2  (3D View)
Global Stoichiometry: Hetero 4-mer - A2B2 

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

Macromolecule Content

• Total Structure Weight: 53.75 kDa 
• Atom Count: 3676 
• Residue Count: 413 
• Unique protein chains: 2

4AZ0

crystal structure of cathepsin a, complexed with 8a.

• DOI: 10.2210/pdb4AZ0/pdb

• Classification: HYDROLASE
• Organism(s): Homo sapiens
• Expression System: Spodoptera frugiperda
• Mutation(s): No 


• Deposited: 2012-06-22 Released: 2012-09-26 
• Deposition Author(s): Ruf, S., Buning, C., Schreuder, H., Horstick, G., Linz, W., Olpp, T., Pernerstorfer, J., Hiss, K., Kroll, K., Kannt, A., Kohlmann, M., Linz, D., Huebschle, T., Ruetten, H., Wirth, K., Schmidt, T., Sadowski, T.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.17 Å

Literature

Novel Beta-Amino Acid Derivatives as Inhibitors of Cathepsin A.

Ruf, S., Buning, C., Schreuder, H., Horstick, G., Linz, W., Olpp, T., Pernerstorfer, J., Hiss, K., Kroll, K., Kannt, A., Kohlmann, M., Linz, D., Hubschle, T., Rutten, H., Wirth, K., Schmidt, T., Sadowski, T.

(2012) J Med Chem 55: 7636

• PubMed: 22861813 
• DOI: 10.1021/jm300663n
• Primary Citation of Related Structures:  
  4AZ0, 4AZ3


• PubMed Abstract: 
  

Cathepsin A (CatA) is a serine carboxypeptidase distributed between lysosomes, cell membrane, and extracellular space. Several peptide hormones including bradykinin and angiotensin I have been described as substrates. Therefore, the inhibition of CatA has the potential for beneficial effects in cardiovascular diseases. Pharmacological inhibition of CatA by the natural product ebelactone B increased renal bradykinin levels and prevented the development of salt-induced hypertension. However, so far no small molecule inhibitors of CatA with oral bioavailability have been described to allow further pharmacological profiling. In our work we identified novel β-amino acid derivatives as inhibitors of CatA after a HTS analysis based on a project adapted fragment approach. The new inhibitors showed beneficial ADME and pharmacokinetic profiles, and their binding modes were established by X-ray crystallography. Further investigations led to the identification of a hitherto unknown pathophysiological role of CatA in cardiac hypertrophy. One of our inhibitors is currently undergoing phase I clinical trials.

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Organizational Affiliation: 

Sanofi-Aventis Deutschland GmbH, Industriepark Höchst, 65926 Frankfurt, Germany. [e-mail]

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
LYSOSOMAL PROTECTIVE PROTEIN 32 KDA CHAIN	A	300	Homo sapiens	Mutation(s): 0  Gene Names: CTSA, PPGB EC: 3.4.16.5
Find proteins for P10619 (Homo sapiens) Explore P10619  Go to UniProtKB:  P10619
NIH Common Fund Data Resources
PHAROS:  P10619 GTEx:  ENSG00000064601

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
LYSOSOMAL PROTECTIVE PROTEIN 20 KDA CHAIN	B	155	Homo sapiens	Mutation(s): 0  Gene Names: CTSA, PPGB EC: 3.4.16.5
Find proteins for P10619 (Homo sapiens) Explore P10619  Go to UniProtKB:  P10619
NIH Common Fund Data Resources
PHAROS:  P10619 GTEx:  ENSG00000064601

Oligosaccharides

Help

Entity ID: 3
Molecule	Chains	Chain Length	2D Diagram	Glycosylation
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	C, D	2		N-Glycosylation

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
S61	A	(S)-3-{[1-(2-Fluoro-phenyl)-5-hydroxy-1H-pyrazole-3-carbonyl]-amino}-3-o-tolyl-propionic acid C20 H18 F N3 O4 DGGLFHJMXJUSDG-HNNXBMFYSA-N
CD	A, B	CADMIUM ION Cd WLZRMCYVCSSEQC-UHFFFAOYSA-N

External Ligand Annotations
ID	Binding Affinity (Sequence Identity %)
S61	IC50 :  38   nM  PDBBind
S61	IC50:  38   nM  BindingDB
S61	IC50:  38   nM  Binding MOAD

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.17 Å
• Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 90.53	α = 90
b = 101.638	β = 101.97
c = 48.179	γ = 90

Software Package:

Software Name	Purpose
BUSTER	refinement
XDS	data reduction
XSCALE	data scaling

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2012-06-22 
• Released Date: 2012-09-26 
Deposition Author(s): Ruf, S., Buning, C., Schreuder, H., Horstick, G., Linz, W., Olpp, T., Pernerstorfer, J., Hiss, K., Kroll, K., Kannt, A., Kohlmann, M., Linz, D., Huebschle, T., Ruetten, H., Wirth, K., Schmidt, T., Sadowski, T.

Revision History 

• Version 1.0: 2012-09-26
  Type: Initial release
  
• Version 1.1: 2019-04-03
  Changes: Data collection, Derived calculations, Experimental preparation, Other
• Version 1.2: 2019-05-08
  Changes: Data collection, Experimental preparation
• Version 2.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Atomic model, Data collection, Derived calculations, Other, Structure summary