3L3N | pdb_00003l3n

Testis ACE co-crystal structure with novel inhibitor lisW


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 
    0.266 (Depositor), 0.267 (DCC) 
  • R-Value Work: 
    0.226 (Depositor), 0.229 (DCC) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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Ligand Structure Quality Assessment 


This is version 2.3 of the entry. See complete history

Literature

Characterization of domain-selective inhibitor binding in angiotensin-converting enzyme using a novel derivative of lisinopril.

Watermeyer, J.M.Kroger, W.L.O'Neill, H.G.Sewell, B.T.Sturrock, E.D.

(2010) Biochem J 428: 67-74

  • DOI: https://doi.org/10.1042/BJ20100056
  • Primary Citation Related Structures: 
    3L3N

  • PubMed Abstract: 

    Human ACE (angiotensin-converting enzyme) (EC 3.4.15.1) is an important drug target because of its role in the regulation of blood pressure via the renin-angiotensin-aldosterone system. Somatic ACE comprises two homologous domains, the differing substrate preferences of which present a new avenue for domain-selective inhibitor design. We have co-crystallized lisW-S, a C-domain-selective derivative of the drug lisinopril, with human testis ACE and determined a structure using X-ray crystallography to a resolution of 2.30 A (1 A=0.1 nm). In this structure, lisW-S is seen to have a similar binding mode to its parent compound lisinopril, but the P2' tryptophan moiety takes a different conformation to that seen in other inhibitors having a tryptophan residue in this position. We have examined further the domain-specific interactions of this inhibitor by mutating C-domain-specific active-site residues to their N domain equivalents, then assessing the effect of the mutation on inhibition by lisW-S using a fluorescence-based assay. Kinetics analysis shows a 258-fold domain-selectivity that is largely due to the co-operative effect of C-domain-specific residues in the S2' subsite. The high affinity and selectivity of this inhibitor make it a good lead candidate for cardiovascular drug development.


  • Organizational Affiliation
    • Division of Medical Biochemistry, Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Observatory, Cape Town, 7935, South Africa.

Macromolecule Content 

  • Total Structure Weight: 69.48 kDa 
  • Atom Count: 4,942 
  • Modeled Residue Count: 575 
  • Deposited Residue Count: 591 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Angiotensin-converting enzyme591Homo sapiensMutation(s): 5 
Gene Names: ACEDCPDCP1
EC: 3.4.15.1 (PDB Primary Data), 3.2.1 (PDB Primary Data)
UniProt & NIH Common Fund Data Resources
Find proteins for P12821 (Homo sapiens)
Explore P12821 
Go to UniProtKB:  P12821
PHAROS:  P12821
GTEx:  ENSG00000159640 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP12821
Glycosylation
Glycosylation Sites: 1Go to GlyGen: P12821-1
Sequence Annotations
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Reference Sequence

Oligosaccharides

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Entity ID: 2
MoleculeChains Length2D Diagram GlycosylationD Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose
B
3N-Glycosylation
Glycosylation Resources
GlyTouCan: G21290RB
GlyCosmos: G21290RB
GlyGen: G21290RB

Small Molecules

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free:  0.266 (Depositor), 0.267 (DCC) 
  • R-Value Work:  0.226 (Depositor), 0.229 (DCC) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 56.383α = 90
b = 84.789β = 90
c = 133.958γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
EPMRphasing
CNSrefinement
PDB_EXTRACTdata extraction
HKL-2000data collection
HKL-2000data 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: 2010-04-28
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2017-11-01
    Changes: Refinement description
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Atomic model, Data collection, Derived calculations, Structure summary
  • Version 2.1: 2021-10-13
    Changes: Database references, Structure summary
  • Version 2.2: 2023-09-06
    Changes: Data collection, Refinement description
  • Version 2.3: 2024-10-30
    Changes: Structure summary