6EN6

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.8 Å
  • R-Value Free: 0.226 
  • R-Value Work: 0.193 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history

Literature

The Design and Development of a Potent and Selective Novel Diprolyl Derivative That Binds to the N-Domain of Angiotensin-I Converting Enzyme.

Fienberg, S.Cozier, G.E.Acharya, K.R.Chibale, K.Sturrock, E.D.

(2018) J. Med. Chem. 61: 344-359

  • DOI: 10.1021/acs.jmedchem.7b01478
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Angiotensin-I converting enzyme (ACE) is a zinc metalloprotease consisting of two catalytic domains (N- and C-). Most clinical ACE inhibitor(s) (ACEi) have been shown to inhibit both domains nonselectively, resulting in adverse effects such as cough ...

    Angiotensin-I converting enzyme (ACE) is a zinc metalloprotease consisting of two catalytic domains (N- and C-). Most clinical ACE inhibitor(s) (ACEi) have been shown to inhibit both domains nonselectively, resulting in adverse effects such as cough and angioedema. Selectively inhibiting the individual domains is likely to reduce these effects and potentially treat fibrosis in addition to hypertension. ACEi from the GVK Biosciences database were inspected for possible N-domain selective binding patterns. From this set, a diprolyl chemical series was modeled using docking simulations. The series was expanded based on key target interactions involving residues known to impart N-domain selectivity. In total, seven diprolyl compounds were synthesized and tested for N-domain selective ACE inhibition. One compound with an aspartic acid in the P2 position (compound 16) displayed potent inhibition (Ki = 11.45 nM) and was 84-fold more selective toward the N-domain. A high-resolution crystal structure of compound 16 in complex with the N-domain revealed the molecular basis for the observed selectivity.


    Organizational Affiliation

    Department of Chemistry, University of Cape Town , Rondebosch 7701, South Africa.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Angiotensin-converting enzyme
A, B, C, D
629Homo sapiensMutation(s): 0 
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 14 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

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A, B, C, D
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
BJ2
Query on BJ2

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A, B, C, D
(2~{S})-1-[(2~{S})-2-[[(1~{S})-1-[(2~{S})-1-[(2~{S})-2-azanyl-4-oxidanyl-4-oxidanylidene-butanoyl]pyrrolidin-2-yl]-2-oxidanyl-2-oxidanylidene-ethyl]amino]propanoyl]pyrrolidine-2-carboxylic acid
C18 H28 N4 O8
AEFOOLCGQAWEBH-JNLQPACOSA-N
 Ligand Interaction
ACT
Query on ACT

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A, B, C, D
ACETATE ION
C2 H3 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-M
 Ligand Interaction
CL
Query on CL

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A, B, C, D
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
FUC
Query on FUC

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A, B, C, D
ALPHA-L-FUCOSE
C6 H12 O5
SHZGCJCMOBCMKK-SXUWKVJYSA-N
 Ligand Interaction
BCN
Query on BCN

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A
BICINE
C6 H13 N O4
FSVCELGFZIQNCK-UHFFFAOYSA-N
 Ligand Interaction
2PE
Query on 2PE

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B
NONAETHYLENE GLYCOL
C18 H38 O10
YZUUTMGDONTGTN-UHFFFAOYSA-N
 Ligand Interaction
EDO
Query on EDO

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A, B, C, D
1,2-ETHANEDIOL
ETHYLENE GLYCOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
 Ligand Interaction
BMA
Query on BMA

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A, B, C, D
BETA-D-MANNOSE
C6 H12 O6
WQZGKKKJIJFFOK-RWOPYEJCSA-N
 Ligand Interaction
MG
Query on MG

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A, B, C, D
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
PGE
Query on PGE

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A, B, D
TRIETHYLENE GLYCOL
C6 H14 O4
ZIBGPFATKBEMQZ-UHFFFAOYSA-N
 Ligand Interaction
XPE
Query on XPE

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B, C
3,6,9,12,15,18,21,24,27-NONAOXANONACOSANE-1,29-DIOL
DECAETHYLENE GLYCOL
C20 H42 O11
DTPCFIHYWYONMD-UHFFFAOYSA-N
 Ligand Interaction
PEG
Query on PEG

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A, B, C, D
DI(HYDROXYETHYL)ETHER
C4 H10 O3
MTHSVFCYNBDYFN-UHFFFAOYSA-N
 Ligand Interaction
NAG
Query on NAG

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A, B, C, D
N-ACETYL-D-GLUCOSAMINE
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.8 Å
  • R-Value Free: 0.226 
  • R-Value Work: 0.193 
  • Space Group: P 1
Unit Cell:
Length (Å)Angle (°)
a = 74.445α = 84.48
b = 103.373β = 85.50
c = 115.646γ = 81.61
Software Package:
Software NamePurpose
PHENIXrefinement
PHASERphasing
Aimlessdata scaling
DIALSdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Medical Research Council (United Kingdom)United KingdomMR/M026647/1

Revision History 

  • Version 1.0: 2018-03-07
    Type: Initial release