1Y8J

Crystal Structure of human NEP complexed with an imidazo[4,5-c]pyridine inhibitor

• PDB DOI: https://doi.org/10.2210/pdb1Y8J/pdb

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


• Deposited: 2004-12-13 Released: 2005-06-07 
• Deposition Author(s): Sahli, S., Frank, B., Schweizer, W.B., Diederich, F., Blum-Kaelin, D., Aebi, J.D., Bohm, H.J., Oefner, C., Dale, G.E.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.25 Å
• R-Value Free: 0.296 
• R-Value Work: 0.226 
• R-Value Observed: 0.230 

Literature

Second-Generation Inhibitors for the Metalloprotease Neprilysin Based on Bicyclic Heteroaromatic Scaffolds: Synthesis, Biological Activity, and X-ray Crystal Structure Analysis

Sahli, S., Frank, B., Schweizer, W.B., Diederich, F., Blum-Kaelin, D., Aebi, J.D., Bohm, H.J., Oefner, C., Dale, G.E.

(2005) Helv Chim Acta 88: 731-750

• DOI: https://doi.org/10.1002/hlca.200590051

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 80.58 kDa 
• Atom Count: 5,873 
• 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

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
STS	G [auth A]	2-[(1S)-1-BENZYL-2-SULFANYLETHYL]-1H-IMIDAZO[4,5-C]PYRIDIN-5-IUM C15 H16 N3 S DCUCDCAIOMIBEA-GFCCVEGCSA-O
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
ACT	F [auth A]	ACETATE ION C2 H3 O2 QTBSBXVTEAMEQO-UHFFFAOYSA-M

Binding Affinity Annotations
ID	Source	Binding Affinity
STS	Binding MOAD:  1Y8J	IC50: 40 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.25 Å
• R-Value Free: 0.296 
• R-Value Work: 0.226 
• R-Value Observed: 0.230 
• Space Group: P 3₂ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 107.355	α = 90
b = 107.356	β = 90
c = 112.466	γ = 120

Software Package:

Software Name	Purpose
REFMAC	refinement
DENZO	data reduction
SCALEPACK	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2005-06-07 
Deposition Author(s): Sahli, S., Frank, B., Schweizer, W.B., Diederich, F., Blum-Kaelin, D., Aebi, J.D., Bohm, H.J., Oefner, C., Dale, G.E.

Revision History  

• Version 1.0: 2005-06-07
  Type: Initial release
  
• Version 1.1: 2008-04-30
  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: 2023-08-23
  Changes: Data collection, Database references, Refinement description, Structure summary