5K1V

Crystal structure of Endoplasmic Reticulum aminopeptidase 2 (ERAP2) in complex with a diaminobenzoic acid derivative ligand.


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.90 Å
  • R-Value Free: 0.273 
  • R-Value Work: 0.205 
  • R-Value Observed: 0.208 

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Ligand Structure Quality Assessment 


This is version 2.0 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:  
    5J6S, 5K1V

  • 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 generation of autoimmunity, thus making ERAP2 a possible pharmacological target for the regulation of adaptive immune responses ...

    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:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Endoplasmic reticulum aminopeptidase 2A, B967Homo sapiensMutation(s): 0 
Gene Names: ERAP2LRAP
EC: 3.4.11
UniProt & NIH Common Fund Data Resources
Find proteins for Q6P179 (Homo sapiens)
Explore Q6P179 
Go to UniProtKB:  Q6P179
PHAROS:  Q6P179
Protein Feature View
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  • Reference Sequence
Oligosaccharides

Help

Entity ID: 2
MoleculeChainsChain Length2D DiagramGlycosylation3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranoseC, D2N-Glycosylation Oligosaccharides Interaction
Glycosylation Resources
GlyTouCan:  G42666HT
GlyCosmos:  G42666HT
GlyGen:  G42666HT
Entity ID: 3
MoleculeChainsChain Length2D DiagramGlycosylation3D Interactions
alpha-D-mannopyranose-(1-4)-alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranoseE4N-Glycosylation Oligosaccharides Interaction
Glycosylation Resources
GlyTouCan:  G81874LD
GlyCosmos:  G81874LD
GlyGen:  G81874LD
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
6PX (Subject of Investigation/LOI)
Query on 6PX

Download Ideal Coordinates CCD File 
G [auth A]methyl N-[4-amino-3-(L-arginylamino)benzene-1-carbonyl]-L-tyrosinate
C23 H31 N7 O5
JECKMXQKZJERLG-HKUYNNGSSA-N
 Ligand Interaction
NAG (Subject of Investigation/LOI)
Query on NAG

Download Ideal Coordinates CCD File 
H [auth A] , I [auth A] , J [auth A] , K [auth A] , L [auth A] , M [auth A] , O [auth B] , P [auth B] , 
H [auth A], I [auth A], J [auth A], K [auth A], L [auth A], M [auth A], O [auth B], P [auth B], Q [auth B], R [auth B], S [auth B], T [auth B]
2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
 Ligand Interaction
ZN
Query on ZN

Download Ideal Coordinates CCD File 
F [auth A], N [auth B]ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.90 Å
  • R-Value Free: 0.273 
  • R-Value Work: 0.205 
  • R-Value Observed: 0.208 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 74.403α = 90
b = 135.171β = 90.15
c = 127.489γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
SCALAdata scaling
MOLREPphasing

Structure Validation

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Ligand Structure Quality Assessment  



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
General Secretariat for Research & TechnologyGreeceERC-14
General Secretariat for Research & TechnologyGreeceHIAP
European Union BioStruct-X283570

Revision History  (Full details and data files)

  • Version 1.0: 2017-03-29
    Type: Initial release
  • Version 1.1: 2017-04-05
    Changes: Database references
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Advisory, Atomic model, Data collection, Derived calculations, Structure summary