3DWB

structure of human ECE-1 complexed with phosphoramidon


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.38 Å
  • R-Value Free: 
    0.345 (Depositor), 0.320 (DCC) 
  • R-Value Work: 
    0.262 (Depositor), 0.250 (DCC) 
  • R-Value Observed: 
    0.266 (Depositor) 

Starting Model: experimental
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Ligand Structure Quality Assessment 

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This is version 1.6 of the entry. See complete history


Literature

Structure of human endothelin-converting enzyme I complexed with phosphoramidon

Schulz, H.Dale, G.E.Karimi-Nejad, Y.Oefner, C.

(2009) J Mol Biol 385: 178-187

  • DOI: https://doi.org/10.1016/j.jmb.2008.10.052
  • Primary Citation of Related Structures:  
    3DWB

  • PubMed Abstract: 

    Endothelin-converting enzyme I (ECE-1) is a mammalian type II integral membrane zinc-containing endopeptidase. ECE-1 catalyzes the final step in the biosynthesis of endothelins in a rate-limiting fashion, through post-translational conversion of the biologically inactive big endothelins. Endothelin-1 overproduction has been implicated in a heterogeneous list of diseases including systemic and pulmonary hypertension, stroke and asthma, cardiac and renal failure. Therefore, ECE-1 is a prime therapeutic target for the regulation of endothelin-1 production in vivo and there is considerable interest in selective inhibitors of this enzyme. Here, we present the crystal structure of the extracellular domain (residues 90-770) of human ECE-1 (C428S) with the generic metalloprotease inhibitor phosphoramidon determined at 2.38 A resolution. The structure is closely related to that of human NEP, providing essential information for a detailed understanding of ligand-binding, specificity determinants as well as selectivity criteria. Selective inhibitors of ECE-1s should have beneficial effects for the treatment of diseases in which an overproduction of ETs plays a pathogenic role.


  • Organizational Affiliation

    Morphochem AG, Basel Switzerland.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Endothelin-converting enzyme 1670Homo sapiensMutation(s): 1 
Gene Names: ECE1
EC: 3.4.24.71
UniProt & NIH Common Fund Data Resources
Find proteins for P42892 (Homo sapiens)
Explore P42892 
Go to UniProtKB:  P42892
PHAROS:  P42892
GTEx:  ENSG00000117298 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP42892
Sequence Annotations
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  • Reference Sequence
Small Molecules
Binding Affinity Annotations 
IDSourceBinding Affinity
RDF BindingDB:  3DWB IC50: min: 0.8, max: 4000 (nM) from 9 assay(s)
Biologically Interesting Molecules (External Reference) 1 Unique
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.38 Å
  • R-Value Free:  0.345 (Depositor), 0.320 (DCC) 
  • R-Value Work:  0.262 (Depositor), 0.250 (DCC) 
  • R-Value Observed: 0.266 (Depositor) 
Space Group: P 61 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 120.88α = 90
b = 120.88β = 90
c = 192.346γ = 120
Software Package:
Software NamePurpose
REFMACrefinement
HKL-2000data collection
DENZOdata reduction
SCALEPACKdata scaling
SHARPphasing

Structure Validation

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Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted RDFClick on this verticalbar to view detailsBest fitted 5HDClick on this verticalbar to view details

Entry History 

Deposition Data

  • Released Date: 2008-11-25 
  • Deposition Author(s): Oefner, C.

Revision History  (Full details and data files)

  • Version 1.0: 2008-11-25
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Advisory, Version format compliance
  • Version 1.2: 2012-12-12
    Changes: Other
  • Version 1.3: 2021-11-10
    Changes: Database references, Derived calculations
  • Version 1.4: 2023-11-01
    Changes: Data collection, Refinement description
  • Version 1.5: 2024-03-20
    Changes: Source and taxonomy
  • Version 1.6: 2024-11-20
    Changes: Structure summary