1DMT

STRUCTURE OF HUMAN NEUTRAL ENDOPEPTIDASE COMPLEXED WITH PHOSPHORAMIDON

• PDB DOI: https://doi.org/10.2210/pdb1DMT/pdb

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


• Deposited: 1999-12-15 Released: 2000-12-20 
• Deposition Author(s): Oefner, C., D'Arcy, A., Hennig, M., Winkler, F.K., Dale, G.E.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free: 0.242 
• R-Value Work: 0.195 
• R-Value Observed: 0.195 

Literature

Structure of human neutral endopeptidase (Neprilysin) complexed with phosphoramidon.

Oefner, C., D'Arcy, A., Hennig, M., Winkler, F.K., Dale, G.E.

(2000) J Mol Biol 296: 341-349

• PubMed: 10669592 
• DOI: https://doi.org/10.1006/jmbi.1999.3492
• Primary Citation of Related Structures:  
  1DMT


• PubMed Abstract: 
  

  Neutral endopeptidase is a mammalian type II integral membrane zinc-containing endopeptidase, which degrades and inactivates a number of bioactive peptides. The range of substrates cleaved by neutral endopeptidase in vitro includes the enkephalins, substance P, endothelin, bradykinin and atrial natriuretic factor. Due to the physiological importance of neutral endopeptidase in the modulation of nociceptive and pressor responses there is considerable interest in inhibitors of this enzyme as novel analgesics and anti-hypertensive agents. Here we describe the crystal structure of the extracellular domain (residues 52-749) of human NEP complexed with the generic metalloproteinase inhibitor phosphoramidon at 2.1 A resolution. The structure reveals two multiply connected folding domains which embrace a large central cavity containing the active site. The inhibitor is bound to one side of this cavity and its binding mode provides a detailed understanding of the ligand-binding and specificity determinants.

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Organizational Affiliation: 

Pharma Preclinical Research, F. Hoffmann-La Roche Ltd., Basel, CH-4070, Switzerland.

Biological Assembly 1  

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

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

Biological Assembly 2  

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

Biological assembly 2 generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 80.89 kDa 
• Atom Count: 6,146 
• Modelled Residue Count: 696 
• Deposited Residue Count: 696 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
NEUTRAL ENDOPEPTIDASE	A	696	Homo sapiens	Mutation(s): 0  EC: 3.4.24.11
UniProt & NIH Common Fund Data Resources
Find proteins for P08473 (Homo sapiens) Go to UniProtKB:  P08473
PHAROS:  P08473 GTEx:  ENSG00000196549
Glycosylation
Glycosylation Sites: 3		Go to GlyGen: P08473-1

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
RDF	F [auth A]	N-ALPHA-L-RHAMNOPYRANOSYLOXY(HYDROXYPHOSPHINYL)-L-LEUCYL-L-TRYPTOPHAN C23 H34 N3 O10 P ZPHBZEQOLSRPAK-XLCYBJAPSA-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
GOL	G [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
ZN	E [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
RDF	BindingDB:  1DMT	Ki: 4 (nM) from 1 assay(s)
		IC50: min: 0.4, max: 200 (nM) from 13 assay(s)
	PDBBind:  1DMT	IC50: 2 (nM) from 1 assay(s)

Biologically Interesting Molecules (External Reference) 1 Unique

Entity ID: 4
ID	Chains	Name	Type/Class	2D Diagram	3D Interactions
PRD_000638 (RDF)	F [auth A]	PHOSPHORAMIDON	Glycopeptide / Enzyme inhibitor

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free: 0.242 
• R-Value Work: 0.195 
• R-Value Observed: 0.195 
• Space Group: P 3₂ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 107.58	α = 90
b = 107.58	β = 90
c = 112.84	γ = 120

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
SHARP	phasing
CNS	refinement

Structure Validation

Entry History 

Deposition Data

• Released Date: 2000-12-20 
Deposition Author(s): Oefner, C., D'Arcy, A., Hennig, M., Winkler, F.K., Dale, G.E.

Revision History  

• Version 1.0: 2000-12-20
  Type: Initial release
  
• Version 1.1: 2008-04-27
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Non-polymer description, Version format compliance
• Version 1.3: 2012-12-12
  Changes: Other
• Version 1.4: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Data collection, Derived calculations, Structure summary
• Version 1.5: 2024-03-13
  Changes: Data collection, Database references, Source and taxonomy, Structure summary