4AZ3

crystal structure of cathepsin a, complexed with 15a


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.04 Å
  • R-Value Free: 0.215 
  • R-Value Work: 0.188 

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Ligand Structure Quality Assessment 


This is version 2.0 of the entry. See complete history


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

  • 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 ...

    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.


    Organizational Affiliation

    Sanofi-Aventis Deutschland GmbH, Industriepark Höchst, 65926 Frankfurt, Germany. sven.ruf@sanofi.com



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
LYSOSOMAL PROTECTIVE PROTEIN 32 KDA CHAINA300Homo sapiensMutation(s): 0 
Gene Names: CTSAPPGB
EC: 3.4.16.5
UniProt & NIH Common Fund Data Resources
Find proteins for P10619 (Homo sapiens)
Explore P10619 
Go to UniProtKB:  P10619
PHAROS:  P10619
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP10619
Protein Feature View
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  • Reference Sequence
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
LYSOSOMAL PROTECTIVE PROTEIN 20 KDA CHAINB155Homo sapiensMutation(s): 0 
Gene Names: CTSAPPGB
EC: 3.4.16.5
UniProt & NIH Common Fund Data Resources
Find proteins for P10619 (Homo sapiens)
Explore P10619 
Go to UniProtKB:  P10619
PHAROS:  P10619
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP10619
Protein Feature View
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  • Reference Sequence
Oligosaccharides

Help

Entity ID: 3
MoleculeChainsChain Length2D DiagramGlycosylation3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranoseC, D 2N-Glycosylation Oligosaccharides Interaction
Glycosylation Resources
GlyTouCan:  G42666HT
GlyCosmos:  G42666HT
GlyGen:  G42666HT
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
S35
Query on S35

Download Ideal Coordinates CCD File 
E [auth A](3S)-3-({[1-(2-fluorophenyl)-5-{[(2R)-2-hydroxy-3,3-dimethylbutyl]oxy}-1H-pyrazol-3-yl]carbonyl}amino)-3-(2-methylphenyl)propanoic acid
C26 H30 F N3 O5
PUJVTKSRQZHCAT-UGKGYDQZSA-N
 Ligand Interaction
CD
Query on CD

Download Ideal Coordinates CCD File 
F [auth A],
G [auth A],
H [auth A],
I [auth B]
CADMIUM ION
Cd
WLZRMCYVCSSEQC-UHFFFAOYSA-N
 Ligand Interaction
Binding Affinity Annotations 
IDSourceBinding Affinity
S35 PDBBind:  4AZ3 IC50: 5 (nM) from 1 assay(s)
BindingDB:  4AZ3 IC50: 5 (nM) from 1 assay(s)
Binding MOAD:  4AZ3 IC50: 5 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.04 Å
  • R-Value Free: 0.215 
  • R-Value Work: 0.188 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 90.59α = 90
b = 102.8β = 101.87
c = 48.39γ = 90
Software Package:
Software NamePurpose
BUSTERrefinement
XDSdata reduction
XSCALEdata scaling

Structure Validation

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Ligand Structure Quality Assessment 



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • 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