2QPJ

Human NEP complexed with a bifunctional NEP/DPP IV inhibitor


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.05 Å
  • R-Value Free: 0.268 
  • R-Value Work: 0.207 
  • R-Value Observed: 0.210 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Structural studies of a bifunctional inhibitor of neprilysin and DPP-IV.

Oefner, C.Pierau, S.Schulz, H.Dale, G.E.

(2007) Acta Crystallogr D Biol Crystallogr 63: 975-981

  • DOI: 10.1107/S0907444907036281
  • Primary Citation of Related Structures:  
    2QPJ

  • PubMed Abstract: 
  • Neutral endopeptidase (NEP) is the major enzyme involved in the metabolic inactivation of a number of bioactive peptides including the enkephalins, substance P, endothelin, bradykinin and atrial natriuretic factor, as well as the incretin hormone glucagon-like peptide 1 (GLP-1), which is a potent stimulator of insulin secretion ...

    Neutral endopeptidase (NEP) is the major enzyme involved in the metabolic inactivation of a number of bioactive peptides including the enkephalins, substance P, endothelin, bradykinin and atrial natriuretic factor, as well as the incretin hormone glucagon-like peptide 1 (GLP-1), which is a potent stimulator of insulin secretion. The activity of GLP-1 is also rapidly abolished by the serine protease dipeptidyl peptidase IV (DPP-IV), which led to an elevated interest in inhibitors of this enzyme for the treatment of type II diabetes. A dual NEP/DPP-IV inhibitor concept is proposed, offering an alternative strategy for the treatment of type 2 diabetes. Here, the synthesis and crystal structures of the soluble extracellular domain of human NEP (residues 52-749) complexed with the NEP, competitive and potent dual NEP/DPP-IV inhibitor MCB3937 are described.


    Organizational Affiliation

    Morphochem AG, CH-4058, Basel, Switzerland.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
NeprilysinA696Homo sapiensMutation(s): 0 
Gene Names: MMEEPN
EC: 3.4.24.11
Find proteins for P08473 (Homo sapiens)
Explore P08473 
Go to UniProtKB:  P08473
NIH Common Fund Data Resources
PHAROS:  P08473
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
I20
Query on I20

Download Ideal Coordinates CCD File 
F [auth A](2S)-2-({(2S)-3-[(R)-[(1R)-1-({(4S)-4-amino-5-[(2S)-2-cyanopyrrolidin-1-yl]-5-oxopentanoyl}amino)ethyl](hydroxy)phosphoryl]-2-benzylpropanoyl}amino)propanoic acid
C25 H36 N5 O7 P
BNNCRIIZOMKDCO-TYIUSFPZSA-N
 Ligand Interaction
NAG
Query on NAG

Download Ideal Coordinates CCD File 
B [auth A], C [auth A], D [auth A]2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
 Ligand Interaction
ZN
Query on ZN

Download Ideal Coordinates CCD File 
E [auth A]ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
I20IC50 :  450   nM  PDBBind
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.05 Å
  • R-Value Free: 0.268 
  • R-Value Work: 0.207 
  • R-Value Observed: 0.210 
  • Space Group: P 32 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 107.123α = 90
b = 107.123β = 90
c = 112.375γ = 120
Software Package:
Software NamePurpose
REFMACrefinement
MAR345dtbdata collection
DENZOdata reduction
SCALEPACKdata scaling
MERLOTphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

  • Deposited Date: 2007-07-24 
  • Released Date: 2007-11-27 
  • Deposition Author(s): Oefner, C., Dale, G.E.

Revision History  (Full details and data files)

  • Version 1.0: 2007-11-27
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Non-polymer description, Version format compliance
  • Version 1.2: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Advisory, Data collection, Derived calculations, Structure summary