6SUK | pdb_00006suk

Crystal structure of Neprilysin in complex with Omapatrilat.


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.75 Å
  • R-Value Free: 
    0.200 (Depositor), 0.206 (DCC) 
  • R-Value Work: 
    0.166 (Depositor), 0.174 (DCC) 
  • R-Value Observed: 
    0.166 (Depositor) 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 1.5 of the entry. See complete history

Literature

Molecular Basis for Omapatrilat and Sampatrilat Binding to Neprilysin-Implications for Dual Inhibitor Design with Angiotensin-Converting Enzyme.

Sharma, U.Cozier, G.E.Sturrock, E.D.Acharya, K.R.

(2020) J Med Chem 63: 5488-5500

  • DOI: https://doi.org/10.1021/acs.jmedchem.0c00441
  • Primary Citation Related Structures: 
    6SUK, 6SVY, 6XVP

  • PubMed Abstract: 

    Neprilysin (NEP) and angiotensin-converting enzyme (ACE) are two key zinc-dependent metallopeptidases in the natriuretic peptide and kinin systems and renin-angiotensin-aldosterone system, respectively. They play an important role in blood pressure regulation and reducing the risk of heart failure. Vasopeptidase inhibitors omapatrilat and sampatrilat possess dual activity against these enzymes by blocking the ACE-dependent conversion of angiotensin I to the potent vasoconstrictor angiotensin II while simultaneously halting the NEP-dependent degradation of vasodilator atrial natriuretic peptide. Here, we report crystal structures of omapatrilat, sampatrilat, and sampatrilat-ASP (a sampatrilat analogue) in complex with NEP at 1.75, 2.65, and 2.6 Å, respectively. A detailed analysis of these structures and the corresponding structures of ACE with these inhibitors has provided the molecular basis of dual inhibitor recognition involving the catalytic site in both enzymes. This new information will be very useful in the design of safer and more selective vasopeptidase inhibitors of NEP and ACE for effective treatment in hypertension and heart failure.


  • Organizational Affiliation
    • Department of Biology and Biochemistry, University of Bath, Claverton Down, Bath BA2 7AY, United Kingdom.

Macromolecule Content 

  • Total Structure Weight: 81.74 kDa 
  • Atom Count: 6,340 
  • Modeled Residue Count: 698 
  • Deposited Residue Count: 699 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Neprilysin699Homo sapiensMutation(s): 0 
Gene Names: MMEEPN
EC: 3.4.24.11
UniProt & NIH Common Fund Data Resources
Find proteins for P08473 (Homo sapiens)
Explore P08473 
Go to UniProtKB:  P08473
PHAROS:  P08473
GTEx:  ENSG00000196549 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP08473
Glycosylation
Glycosylation Sites: 4Go to GlyGen: P08473-1
Sequence Annotations
Expand
Reference Sequence

Small Molecules

Ligands 5 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
FT8
(Subject of Investigation/LOI)

Query on FT8



Download:Ideal Coordinates CCD File
G [auth A]Omapatrilat
C19 H24 N2 O4 S2
LVRLSYPNFFBYCZ-VGWMRTNUSA-N
NAG

Query on NAG



Download:Ideal Coordinates CCD File
C [auth A],
D [auth A],
E [auth A],
F [auth A]
2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
PEG

Query on PEG



Download:Ideal Coordinates CCD File
H [auth A],
L [auth A]
DI(HYDROXYETHYL)ETHER
C4 H10 O3
MTHSVFCYNBDYFN-UHFFFAOYSA-N
ZN

Query on ZN



Download:Ideal Coordinates CCD File
B [auth A]ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
EDO

Query on EDO



Download:Ideal Coordinates CCD File
I [auth A],
J [auth A],
K [auth A],
M [auth A]
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
Binding Affinity Annotations 
IDSourceBinding Affinity
FT8 BindingDB:  6SUK Ki: 9 (nM) from 1 assay(s)
IC50: min: 0.2, max: 9 (nM) from 3 assay(s)

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.75 Å
  • R-Value Free:  0.200 (Depositor), 0.206 (DCC) 
  • R-Value Work:  0.166 (Depositor), 0.174 (DCC) 
  • R-Value Observed: 0.166 (Depositor) 
Space Group: P 32 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 107.935α = 90
b = 107.935β = 90
c = 112.841γ = 120
Software Package:
Software NamePurpose
PHENIXrefinement
PHENIXrefinement
DIALSdata reduction
Aimlessdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

& Funding Information

Deposition Data


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

Revision History  (Full details and data files)

  • Version 1.0: 2020-05-13
    Type: Initial release
  • Version 1.1: 2020-05-20
    Changes: Database references
  • Version 1.2: 2020-06-10
    Changes: Database references
  • Version 1.3: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Data collection, Derived calculations, Structure summary
  • Version 1.4: 2024-01-24
    Changes: Data collection, Database references, Refinement description, Structure summary
  • Version 1.5: 2024-10-23
    Changes: Structure summary