2YB9

Crystal Structure of Human Neutral Endopeptidase complexed with a heteroarylalanine diacid.

• PDB DOI: https://doi.org/10.2210/pdb2YB9/pdb

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


• Deposited: 2011-03-02 Released: 2011-05-25 
• Deposition Author(s): Glossop, M.S., Bazin, R.J., Dack, K.N., Done, S., Fox, D.N.A., MacDonald, G.A., Mills, M., Owen, D.R., Phillips, C., Reeves, K.A., Ringer, T.J., Strang, R.S., Watson, C.A.L.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Free: 0.243 
• R-Value Work: 0.172 
• R-Value Observed: 0.176 

Literature

Synthesis and Evaluation of Heteroarylalanine Diacids as Potent and Selective Neutral Endopeptidase Inhibitors.

Glossop, M.S., Bazin, R.J., Dack, K.N., Fox, D.N.A., Macdonald, G.A., Mills, M., Owen, D.R., Phillips, C., Reeves, K.A., Ringer, T.J., Strang, R.S., Watson, C.A.L.

(2011) Bioorg Med Chem Lett 21: 3404

• PubMed: 21515054 
• DOI: https://doi.org/10.1016/j.bmcl.2011.03.109
• Primary Citation of Related Structures:  
  2YB9


• PubMed Abstract: 
  

  Heteroarylalanine derivatives 4 were designed as potential inhibitors of neutral endopeptidase (NEP EC 3.4.24.11). Selectivity over other zinc metalloproteinases was explored through occupation of the S2' subsite within NEP. Structural optimisation led to the identification of 5-phenyl oxazole 4f, a potent and selective NEP inhibitor. A crystal structure of the inhibitor bound complex is reported.

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Organizational Affiliation: 

Pfizer Global Research and Development, Ramsgate Road, Sandwich CT13 9NJ, UK. [e-mail]

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 80.03 kDa 
• Atom Count: 6,110 
• 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  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 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
HA0	C [auth A]	HETEROARYLALANINE 5-PHENYL OXAZOLE C24 H30 N2 O6 SFZJKCPBOHKUKC-QZTJIDSGSA-N
ZN	B [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
HA0	PDBBind:  2YB9	IC50: 0.6 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Free: 0.243 
• R-Value Work: 0.172 
• R-Value Observed: 0.176 
• Space Group: P 3₂ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 107.841	α = 90
b = 107.841	β = 90
c = 112.794	γ = 120

Software Package:

Software Name	Purpose
BUSTER	refinement

Structure Validation

Entry History 

Deposition Data

• Released Date: 2011-05-25 
Deposition Author(s): Glossop, M.S., Bazin, R.J., Dack, K.N., Done, S., Fox, D.N.A., MacDonald, G.A., Mills, M., Owen, D.R., Phillips, C., Reeves, K.A., Ringer, T.J., Strang, R.S., Watson, C.A.L.

Revision History  

• Version 1.0: 2011-05-25
  Type: Initial release
  
• Version 1.1: 2011-11-02
  Changes: Database references, Version format compliance