5J6S

Crystal structure of Endoplasmic Reticulum Aminopeptidase 2 (ERAP2) in complex with a hydroxamic derivative ligand


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.8 Å
  • R-Value Free: 0.276 
  • R-Value Work: 0.205 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Crystal Structures of ERAP2 Complexed with Inhibitors Reveal Pharmacophore Requirements for Optimizing Inhibitor Potency.

Mpakali, A.Giastas, P.Deprez-Poulain, R.Papakyriakou, A.Koumantou, D.Gealageas, R.Tsoukalidou, S.Vourloumis, D.Mavridis, I.M.Stratikos, E.Saridakis, E.

(2017) ACS Med Chem Lett 8: 333-337

  • DOI: 10.1021/acsmedchemlett.6b00505
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Endoplasmic reticulum aminopeptidase 2 assists with the generation of antigenic peptides for presentation onto Major Histocompatibility Class I molecules in humans. Recent evidence has suggested that the activity of ERAP2 may contribute to the genera ...

    Endoplasmic reticulum aminopeptidase 2 assists with the generation of antigenic peptides for presentation onto Major Histocompatibility Class I molecules in humans. Recent evidence has suggested that the activity of ERAP2 may contribute to the generation of autoimmunity, thus making ERAP2 a possible pharmacological target for the regulation of adaptive immune responses. To better understand the structural elements of inhibitors that govern their binding affinity to the ERAP2 active site, we cocrystallized ERAP2 with a medium activity 3,4-diaminobenzoic acid inhibitor and a poorly active hydroxamic acid derivative. Comparison of these two crystal structures with a previously solved structure of ERAP2 in complex with a potent phosphinic pseudopeptide inhibitor suggests that engaging the substrate N-terminus recognition properties of the active site is crucial for inhibitor binding even in the absence of a potent zinc-binding group. Proper utilization of all five major pharmacophores is necessary, however, to optimize inhibitor potency.


    Organizational Affiliation

    National Center for Scientific Research Demokritos , Agia Paraskevi, GR-15310 Athens, Greece.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Endoplasmic reticulum aminopeptidase 2
A, B
967Homo sapiensMutation(s): 0 
Gene Names: ERAP2 (LRAP)
EC: 3.4.11.-
Find proteins for Q6P179 (Homo sapiens)
Go to Gene View: ERAP2
Go to UniProtKB:  Q6P179
Small Molecules
Ligands 5 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

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Download CCD File 
A, B
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
MAN
Query on MAN

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Download CCD File 
B
ALPHA-D-MANNOSE
C6 H12 O6
WQZGKKKJIJFFOK-PQMKYFCFSA-N
 Ligand Interaction
BMA
Query on BMA

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Download CCD File 
A, B
BETA-D-MANNOSE
C6 H12 O6
WQZGKKKJIJFFOK-RWOPYEJCSA-N
 Ligand Interaction
6GA
Query on 6GA

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Download CCD File 
A, B
(2S)-N~1~-benzyl-2-[(4-fluorophenyl)methyl]-N~3~-hydroxypropanediamide
C17 H17 F N2 O3
UBULRDFJXZRBJH-HNNXBMFYSA-N
 Ligand Interaction
NAG
Query on NAG

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Download CCD File 
A, B
N-ACETYL-D-GLUCOSAMINE
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.8 Å
  • R-Value Free: 0.276 
  • R-Value Work: 0.205 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 73.540α = 90.00
b = 134.330β = 91.71
c = 127.580γ = 90.00
Software Package:
Software NamePurpose
PHASERphasing
iMOSFLMdata reduction
SCALAdata scaling
PHENIXrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
European Union and the Greek Secretariat for Research and Technology (Bilateral Greece-France collaboration action)GreeceHIAP

Revision History 

  • Version 1.0: 2017-03-15
    Type: Initial release
  • Version 1.1: 2017-04-05
    Type: Database references