Tesis ACE co-crystal structure with ketone ACE inhibitor kAF

Experimental Data Snapshot

  • Resolution: 2.17 Å
  • R-Value Free: 0.251 
  • R-Value Work: 0.202 

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Probing the basis of domain-dependent inhibition using novel ketone inhibitors of Angiotensin-converting enzyme

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

(2008) Biochemistry 47: 5942-5950

  • DOI: https://doi.org/10.1021/bi8002605
  • Primary Citation of Related Structures:  
    3BKK, 3BKL

  • PubMed Abstract: 

    Human angiotensin-converting enzyme (ACE) has two homologous domains, the N and C domains, with differing substrate preferences. X-ray crystal structures of the C and N domains complexed with various inhibitors have allowed identification of active site residues that might be important for the molecular basis of this selectivity. However, it is unclear to what extent the different residues contribute to substrate domain selectivity. Here, cocrystal structures of human testis ACE, equivalent to the C domain, have been determined with two novel C domain-selective ketomethylene inhibitors, (5 S)-5-[( N-benzoyl)amino]-4-oxo-6-phenylhexanoyl- l-tryptophan (kAW) and (5 S)-5-[( N-benzoyl)amino]-4-oxo-6-phenylhexanoyl- l-phenylalanine (kAF). The ketone groups of both inhibitors bind to the zinc ion as a hydrated geminal diolate, demonstrating the ability of the active site to catalyze the formation of the transition state. Moreover, active site residues involved in inhibitor binding have been mutated to their N domain counterparts, and the effect of the mutations on inhibitor binding has been determined. The C domain selectivity of these inhibitors was found to result from interactions between bulky hydrophobic side chain moieties and C domain-specific residues F391, V518, E376, and V380 (numbering of testis ACE). Mutation of these residues decreased the affinity for the inhibitors 4-20-fold. T282, V379, E403, D453, and S516 did not contribute individually to C domain-selective inhibitor binding. Further domain-selective inhibitor design should focus on increasing both the affinity and selectivity of the side chain moieties.

  • Organizational Affiliation

    Division of Medical Biochemistry, Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Observatory 7925, South Africa.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Angiotensin-converting enzyme, somatic isoform591Homo sapiensMutation(s): 5 
Gene Names: ACEDCPDCP1
UniProt & NIH Common Fund Data Resources
Find proteins for P12821 (Homo sapiens)
Explore P12821 
Go to UniProtKB:  P12821
PHAROS:  P12821
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP12821
Sequence Annotations
  • Reference Sequence


Entity ID: 2
MoleculeChains Length2D Diagram Glycosylation3D Interactions
Glycosylation Resources
GlyTouCan:  G21290RB
GlyCosmos:  G21290RB
GlyGen:  G21290RB
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on KAF

Download Ideal Coordinates CCD File 
H [auth A]N-{(5S)-4,4-dihydroxy-6-phenyl-5-[(phenylcarbonyl)amino]hexanoyl}-L-phenylalanine
C28 H30 N2 O6
Query on NAG

Download Ideal Coordinates CCD File 
C [auth A],
D [auth A]
C8 H15 N O6
Query on ZN

Download Ideal Coordinates CCD File 
E [auth A]ZINC ION
Query on CL

Download Ideal Coordinates CCD File 
F [auth A],
G [auth A]
Binding Affinity Annotations 
IDSourceBinding Affinity
KAF PDBBind:  3BKK Ki: 830 (nM) from 1 assay(s)
Binding MOAD:  3BKK Ki: 830 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Resolution: 2.17 Å
  • R-Value Free: 0.251 
  • R-Value Work: 0.202 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 60.383α = 90
b = 85.07β = 90
c = 135.506γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
PDB_EXTRACTdata extraction
HKL-2000data collection
HKL-2000data reduction
HKL-2000data 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: 2008-06-10
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Non-polymer description, Version format compliance
  • Version 1.2: 2017-10-25
    Changes: Refinement description, Source and taxonomy
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Atomic model, Data collection, Derived calculations, Structure summary
  • Version 2.1: 2021-10-20
    Changes: Database references, Structure summary
  • Version 2.2: 2023-08-30
    Changes: Data collection, Refinement description