6T6R

Human endoplasmic reticulum aminopeptidase 1 (ERAP1) in complex with (4aR,5S,6R,8S,8aR)-5-(2-(Furan-3-yl)ethyl)-8-hydroxy-5,6,8a-trimethyl-3,4,4a,5,6,7,8,8a-octahydronaphthalene-1-carboxylic acid


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.67 Å
  • R-Value Free: 0.194 
  • R-Value Work: 0.169 
  • R-Value Observed: 0.170 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Targeting the Regulatory Site of ER Aminopeptidase 1 Leads to the Discovery of a Natural Product Modulator of Antigen Presentation.

Liddle, J.Hutchinson, J.P.Kitchen, S.Rowland, P.Neu, M.Cecconie, T.Holmes, D.S.Jones, E.Korczynska, J.Koumantou, D.Lea, J.D.Nickels, L.Pemberton, M.Phillipou, A.Schneck, J.L.Sheehan, H.Tinworth, C.P.Uings, I.Wojno-Picon, J.Young, R.J.Stratikos, E.

(2020) J Med Chem 63: 3348-3358

  • DOI: 10.1021/acs.jmedchem.9b02123
  • Primary Citation of Related Structures:  
    6T6R

  • PubMed Abstract: 
  • ER aminopeptidase 1 (ERAP1) is an intracellular enzyme that generates antigenic peptides and is an emerging target for cancer immunotherapy and the control of autoimmunity. ERAP1 inhibitors described previously target the active site and are limited in s ...

    ER aminopeptidase 1 (ERAP1) is an intracellular enzyme that generates antigenic peptides and is an emerging target for cancer immunotherapy and the control of autoimmunity. ERAP1 inhibitors described previously target the active site and are limited in selectivity, minimizing their clinical potential. To address this, we targeted the regulatory site of ERAP1 using a high-throughput screen and discovered a small molecule hit that is highly selective for ERAP1. (4a R ,5 S ,6 R ,8 S ,8a R )-5-(2-(Furan-3-yl)ethyl)-8-hydroxy-5,6,8a-trimethyl-3,4,4a,5,6,7,8,8a-octahydronaphthalene-1-carboxylic acid is a natural product found in Dodonaea viscosa that constitutes a submicromolar, highly selective, and cell-active modulator of ERAP1. Although the compound activates hydrolysis of small model substrates, it is a competitive inhibitor for physiologically relevant longer peptides. Crystallographic analysis confirmed that the compound targets the regulatory site of the enzyme that normally binds the C-terminus of the peptide substrate. Our findings constitute a novel starting point for the development of selective ERAP1 modulators that have potential for further clinical development.


    Organizational Affiliation

    National Centre for Scientific Research "Demokritos", Patriarchou Gregoriou and Neapoleos 27, Agia Paraskevi, Athens 15341, Greece.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Endoplasmic reticulum aminopeptidase 1 A922Homo sapiensMutation(s): 4 
Gene Names: ERAP1APPILSARTS1KIAA0525UNQ584/PRO1154
EC: 3.4.11
Find proteins for Q9NZ08 (Homo sapiens)
Explore Q9NZ08 
Go to UniProtKB:  Q9NZ08
NIH Common Fund Data Resources
PHAROS:  Q9NZ08
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MNZ
Query on MNZ

Download Ideal Coordinates CCD File 
A
(4~{a}~{R},5~{S},6~{R},8~{S},8~{a}~{R})-5-[2-(furan-3-yl)ethyl]-5,6,8~{a}-trimethyl-8-oxidanyl-3,4,4~{a},6,7,8-hexahydronaphthalene-1-carboxylic acid
C20 H28 O4
XWKYXEIGWQYOCY-KWLVRGKZSA-N
 Ligand Interaction
MLT
Query on MLT

Download Ideal Coordinates CCD File 
A
D-MALATE
C4 H6 O5
BJEPYKJPYRNKOW-UWTATZPHSA-N
 Ligand Interaction
ZN
Query on ZN

Download Ideal Coordinates CCD File 
A
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
EDO
Query on EDO

Download Ideal Coordinates CCD File 
A
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.67 Å
  • R-Value Free: 0.194 
  • R-Value Work: 0.169 
  • R-Value Observed: 0.170 
  • Space Group: P 21 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 113.22α = 90
b = 140.26β = 90
c = 57.92γ = 90
Software Package:
Software NamePurpose
BUSTERrefinement
PDB_EXTRACTdata extraction
DIALSdata reduction
Aimlessdata scaling
BUSTERphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

  • Deposited Date: 2019-10-18 
  • Released Date: 2020-03-18 
  • Deposition Author(s): Rowland, P.

Revision History 

  • Version 1.0: 2020-03-18
    Type: Initial release
  • Version 1.1: 2020-04-08
    Changes: Database references