4BXK

Crystal structure of the Angiotensin-1 converting enzyme N-domain in complex with a domain-specific inhibitor


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.2 Å
  • R-Value Free: 0.220 
  • R-Value Work: 0.187 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Fragment-Based Design for the Development of N-Domain Selective Angiotensin-1 Converting Enzyme Inhibitors

Sharma, R.K.Masuyer, G.Lubbe, L.Zamora, I.Acharya, K.R.Chibale, K.Sturrock, E.D.Douglas, R.G.

(2014) Clin.Sci. 126: 305

  • DOI: 10.1042/CS20130403

  • PubMed Abstract: 
  • ACE (angiotensin-1-converting enzyme) is a zinc metallopeptidase that plays a prominent role in blood pressure regulation and electrolyte homeostasis. ACE consists of two homologous domains that despite similarities of sequence and topology display d ...

    ACE (angiotensin-1-converting enzyme) is a zinc metallopeptidase that plays a prominent role in blood pressure regulation and electrolyte homeostasis. ACE consists of two homologous domains that despite similarities of sequence and topology display differences in substrate processing and inhibitor binding. The design of inhibitors that selectively inhibit the N-domain (N-selective) could be useful in treating conditions of tissue injury and fibrosis due to build-up of N-domain-specific substrate Ac-SDKP (N-acetyl-Ser-Asp-Lys-Pro). Using a receptor-based SHOP (scaffold hopping) approach with N-selective inhibitor RXP407, a shortlist of scaffolds that consisted of modified RXP407 backbones with novel chemotypes was generated. These scaffolds were selected on the basis of enhanced predicted interaction energies with N-domain residues that differed from their C-domain counterparts. One scaffold was synthesized and inhibitory binding tested using a fluorogenic ACE assay. A molecule incorporating a tetrazole moiety in the P2 position (compound 33RE) displayed potent inhibition (K(i)=11.21±0.74 nM) and was 927-fold more selective for the N-domain than the C-domain. A crystal structure of compound 33RE in complex with the N-domain revealed its mode of binding through aromatic stacking with His388 and a direct hydrogen bond with the hydroxy group of the N-domain specific Tyr369. This work further elucidates the molecular basis for N-domain-selective inhibition and assists in the design of novel N-selective ACE inhibitors that could be employed in treatment of fibrosis disorders.


    Organizational Affiliation

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




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
ANGIOTENSIN-CONVERTING ENZYME
A, B
629Homo sapiensMutation(s): 8 
Gene Names: ACE (DCP, DCP1)
EC: 3.2.1.-, 3.4.15.1
Find proteins for P12821 (Homo sapiens)
Go to Gene View: ACE
Go to UniProtKB:  P12821
Small Molecules
Ligands 9 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download SDF File 
Download CCD File 
A, B
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
CL
Query on CL

Download SDF File 
Download CCD File 
A, B
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
1IU
Query on 1IU

Download SDF File 
Download CCD File 
A, B
[3-[[(2S)-1-azanyl-1-oxidanylidene-propan-2-yl]amino]-2-methyl-3-oxidanylidene-propyl]-[(1R)-1-[[(2R)-2-azanyl-3-(1H-1,2,3,4-tetrazol-5-yl)propanoyl]amino]-2-phenyl-ethyl]phosphinic acid
C19 H29 N8 O5 P
RAFOALGGQUIRNB-FAXLKDOZSA-N
 Ligand Interaction
FUC
Query on FUC

Download SDF File 
Download CCD File 
A
ALPHA-L-FUCOSE
C6 H12 O5
SHZGCJCMOBCMKK-SXUWKVJYSA-N
 Ligand Interaction
BMA
Query on BMA

Download SDF File 
Download CCD File 
A, B
BETA-D-MANNOSE
C6 H12 O6
WQZGKKKJIJFFOK-RWOPYEJCSA-N
 Ligand Interaction
PG4
Query on PG4

Download SDF File 
Download CCD File 
B
TETRAETHYLENE GLYCOL
C8 H18 O5
UWHCKJMYHZGTIT-UHFFFAOYSA-N
 Ligand Interaction
P6G
Query on P6G

Download SDF File 
Download CCD File 
A, B
HEXAETHYLENE GLYCOL
POLYETHYLENE GLYCOL PEG400
C12 H26 O7
IIRDTKBZINWQAW-UHFFFAOYSA-N
 Ligand Interaction
PEG
Query on PEG

Download SDF File 
Download CCD File 
A, B
DI(HYDROXYETHYL)ETHER
C4 H10 O3
MTHSVFCYNBDYFN-UHFFFAOYSA-N
 Ligand Interaction
NAG
Query on NAG

Download SDF File 
Download CCD File 
A, B
N-ACETYL-D-GLUCOSAMINE
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
1IUKi: 11.21 nM BINDINGMOAD
1IUKi: 11.21 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.2 Å
  • R-Value Free: 0.220 
  • R-Value Work: 0.187 
  • Space Group: P 1
Unit Cell:
Length (Å)Angle (°)
a = 73.142α = 88.43
b = 77.255β = 64.28
c = 82.866γ = 75.29
Software Package:
Software NamePurpose
REFMACrefinement
SCALAdata scaling
XDSdata reduction
PHASERphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2013-09-18
    Type: Initial release
  • Version 1.1: 2013-09-25
    Type: Database references, Derived calculations
  • Version 1.2: 2013-11-06
    Type: Database references
  • Version 1.3: 2013-11-13
    Type: Atomic model, Derived calculations, Other, Refinement description