6I6Z

Crystal structure of the human CARBOXYPEPTIDASE A1 in complex with the PHOSPHINIC INHIBITOR Acetyl-Tyr-Ala-Y(PO2CH2)-homoPhe-OH


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.72 Å
  • R-Value Free: 0.183 
  • R-Value Work: 0.158 
  • R-Value Observed: 0.160 

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This is version 2.3 of the entry. See complete history


Literature

Synthesis and Structural/Functional Characterization of Selective M14 Metallocarboxypeptidase Inhibitors Based on Phosphinic Pseudopeptide Scaffold: Implications on the Design of Specific Optical Probes.

Covaleda, G.Gallego, P.Vendrell, J.Georgiadis, D.Lorenzo, J.Dive, V.Aviles, F.X.Reverter, D.Devel, L.

(2019) J Med Chem 62: 1917-1931

  • DOI: https://doi.org/10.1021/acs.jmedchem.8b01465
  • Primary Citation of Related Structures:  
    6I6Z

  • PubMed Abstract: 

    Metallocarboxypeptidases (MCPs) of the M14 family are Zn 2+ -dependent exoproteases present in almost every tissue or fluid in mammals. These enzymes perform a large variety of physiological functions and are involved in several pathologies, such as pancreatic diseases, inflammation, fibrinolysis, and cancer. Here, we describe the synthesis and functional/structural characterization of a series of reversible tight-binding phosphinic pseudopeptide inhibitors that show high specificity and potency toward these proteases. Characterization of their inhibitory potential against a large variety of MCPs, combined with high-resolution crystal structures of three selected candidates in complex with human carboxypeptidase A (CPA)1, allowed to decipher the structural determinants governing selectivity for type-A of the M14A MCP family. Further, the phosphinic pseudopeptide framework was exploited to generate an optical probe selectively targeting human CPAs. The phosphinic pseudopeptides presented here constitute the first example of chemical probes useful to selectively report on type-A MCPs activity in complex media.


  • Organizational Affiliation

    Institut de Biotecnologia i de Biomedicina and Departament de Bioquímica i de Biologia Molecular , Universitat Autònoma de Barcelona , Bellaterra, 08193 Barcelona , Spain.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Carboxypeptidase A1
A, B
308Homo sapiensMutation(s): 0 
Gene Names: CPA1CPA
EC: 3.4.17.1
UniProt & NIH Common Fund Data Resources
Find proteins for P15085 (Homo sapiens)
Explore P15085 
Go to UniProtKB:  P15085
PHAROS:  P15085
GTEx:  ENSG00000091704 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP15085
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.72 Å
  • R-Value Free: 0.183 
  • R-Value Work: 0.158 
  • R-Value Observed: 0.160 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 46.121α = 90
b = 84.109β = 90
c = 158.195γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
MOLREPphasing
SCALAdata scaling
XDSdata reduction

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2018-12-12
    Type: Initial release
  • Version 2.0: 2019-01-23
    Changes: Atomic model, Data collection, Database references, Derived calculations, Polymer sequence, Source and taxonomy, Structure summary
  • Version 2.1: 2019-02-06
    Changes: Data collection, Database references
  • Version 2.2: 2019-03-13
    Changes: Data collection, Database references
  • Version 2.3: 2024-01-24
    Changes: Data collection, Database references, Derived calculations, Refinement description