1R1J

STRUCTURAL ANALYSIS OF NEPRILYSIN WITH VARIOUS SPECIFIC AND POTENT INHIBITORS

• PDB DOI: https://doi.org/10.2210/pdb1R1J/pdb

• Classification: HYDROLASE
• Organism(s): Homo sapiens
• Expression System: Saccharomyces cerevisiae
• Mutation(s): No 


• Deposited: 2003-09-24 Released: 2004-09-28 
• Deposition Author(s): Oefner, C., Roques, B.P., Fournie-Zaluski, M.C., Dale, G.E.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.35 Å
• R-Value Free: 0.283 
• R-Value Work: 0.222 
• R-Value Observed: 0.225 

Literature

Structural analysis of neprilysin with various specific and potent inhibitors.

Oefner, C., Roques, B.P., Fournie-Zaluski, M.C., Dale, G.E.

(2004) Acta Crystallogr D Biol Crystallogr 60: 392-396

• PubMed: 14747736 
• DOI: https://doi.org/10.1107/S0907444903027410
• Primary Citation of Related Structures:  
  1R1H, 1R1I, 1R1J


• 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. Owing to the physiological importance of NEP in the modulation of nociceptive and pressor responses, there is considerable interest in inhibitors of this enzyme as novel analgesics and antihypertensive agents. Here, the crystal structures of the soluble extracellular domain of human NEP (residues 52-749) complexed with various potent and competitive inhibitors are described. The structures unambiguously reveal the binding mode of the different zinc-chelating groups and the subsite specificity of the enzyme.

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Organizational Affiliation: 

Morphochem AG, CH-4058 Basel, Switzerland.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 80.66 kDa 
• Atom Count: 5,754 
• Modelled Residue Count: 696 
• Deposited Residue Count: 696 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Neprilysin	A	696	Homo sapiens	Mutation(s): 0  Gene Names: MME, EPN 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
Glycosylation
Glycosylation Sites: 3		Go to GlyGen: P08473-1

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
OIR	F [auth A]	N-(3-PHENYL-2-SULFANYLPROPANOYL)PHENYLALANYLALANINE C21 H24 N2 O4 S CNILVMARPONFBX-JCGIZDLHSA-N
NAG	B [auth A], C [auth A], D [auth A]	2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N
ZN	E [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
OIR	PDBBind:  1R1J	Ki: 2.3 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.35 Å
• R-Value Free: 0.283 
• R-Value Work: 0.222 
• R-Value Observed: 0.225 
• Space Group: P 3₂ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 107.458	α = 90
b = 107.458	β = 90
c = 111.997	γ = 120

Software Package:

Software Name	Purpose
REFMAC	refinement
DENZO	data reduction
SCALEPACK	data scaling
AMoRE	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2004-09-28 
Deposition Author(s): Oefner, C., Roques, B.P., Fournie-Zaluski, M.C., Dale, G.E.

Revision History  

• Version 1.0: 2004-09-28
  Type: Initial release
  
• Version 1.1: 2008-04-29
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Non-polymer description, Version format compliance
• Version 1.3: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Data collection, Derived calculations, Structure summary
• Version 1.4: 2024-10-30
  Changes: Data collection, Database references, Structure summary