8CGW | pdb_00008cgw

Insulin-regulated aminopeptidase (IRAP) in complex with an allosteric benzopyran-based inhibitor


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.03 Å
  • R-Value Free: 
    0.242 (Depositor), 0.245 (DCC) 
  • R-Value Work: 
    0.203 (Depositor), 0.203 (DCC) 
  • R-Value Observed: 
    0.205 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history

Literature

Mechanisms of Allosteric Inhibition of Insulin-Regulated Aminopeptidase.

Mpakali, A.Barla, I.Lu, L.Ramesh, K.M.Thomaidis, N.Stern, L.J.Giastas, P.Stratikos, E.

(2024) J Mol Biology 436: 168449-168449

  • DOI: https://doi.org/10.1016/j.jmb.2024.168449
  • Primary Citation Related Structures: 
    8CGP, 8CGW

  • PubMed Abstract: 

    Inhibition of Insulin-Regulated Aminopeptidase is being actively explored for the treatment of several human diseases and several classes of inhibitors have been developed although no clinical applications have been reported yet. Here, we combine enzymological analysis with x-ray crystallography to investigate the mechanism employed by two of the most studied inhibitors of IRAP, an aryl sulfonamide and a 2-amino-4H-benzopyran named HFI-419. Although both compounds have been hypothesized to target the enzyme's active site by competitive mechanisms, we discovered that they instead target previously unidentified proximal allosteric sites and utilize non-competitive inhibition mechanisms. X-ray crystallographic analysis demonstrated that the aryl sulfonamide stabilizes the closed, more active, conformation of the enzyme whereas HFI-419 locks the enzyme in a semi-open, and likely less active, conformation. HFI-419 potency is substrate-dependent and fails to effectively block the degradation of the physiological substrate cyclic peptide oxytocin. Our findings demonstrate alternative mechanisms for inhibiting IRAP through allosteric sites and conformational restricting and suggest that the pharmacology of HFI-419 may be more complicated than initially considered. Such conformation-specific interactions between IRAP and small molecules can be exploited for the design of more effective second-generation allosteric inhibitors.


  • Organizational Affiliation
    • Laboratory of Biochemistry, Department of Chemistry, National and Kapodistrian University of Athens, Athens 15771, Greece; National Centre for Scientific Research Demokritos, Athens 15341, Greece.

Macromolecule Content 

  • Total Structure Weight: 211.45 kDa 
  • Atom Count: 14,531 
  • Modeled Residue Count: 1,711 
  • Deposited Residue Count: 1,746 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Leucyl-cystinyl aminopeptidase, pregnancy serum form
A, B
873Homo sapiensMutation(s): 0 
Gene Names: LNPEPOTASE
EC: 3.4.11.3
UniProt & NIH Common Fund Data Resources
Find proteins for Q9UIQ6 (Homo sapiens)
Explore Q9UIQ6 
Go to UniProtKB:  Q9UIQ6
PHAROS:  Q9UIQ6
GTEx:  ENSG00000113441 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9UIQ6
Glycosylation
Glycosylation Sites: 10Go to GlyGen: Q9UIQ6-1
Sequence Annotations
Expand
Reference Sequence

Oligosaccharides

Help  
Entity ID: 2
MoleculeChains Length2D Diagram GlycosylationD Interactions
beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
C, D, H, I, L
3N-Glycosylation
Glycosylation Resources
GlyTouCan: G15407YE
GlyCosmos: G15407YE
GlyGen: G15407YE
Entity ID: 3
MoleculeChains Length2D Diagram GlycosylationD Interactions
alpha-D-mannopyranose-(1-3)-alpha-D-mannopyranose-(1-6)-[alpha-D-mannopyranose-(1-3)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
E
6N-Glycosylation
Glycosylation Resources
GlyTouCan: G09724ZC
GlyCosmos: G09724ZC
GlyGen: G09724ZC
Entity ID: 4
MoleculeChains Length2D Diagram GlycosylationD Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
F, K, M, N
2N-Glycosylation
Glycosylation Resources
GlyTouCan: G42666HT
GlyCosmos: G42666HT
GlyGen: G42666HT
Entity ID: 5
MoleculeChains Length2D Diagram GlycosylationD Interactions
alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
G, J
4N-Glycosylation
Glycosylation Resources
GlyTouCan: G81315DD
GlyCosmos: G81315DD
GlyGen: G81315DD

Small Molecules

Ligands 6 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
UJX
(Subject of Investigation/LOI)

Query on UJX



Download:Ideal Coordinates CCD File
P [auth A] ethyl 2-acetamido-7-hydroxy-4-(pyridin-3-yl)-4H-chromene-3-carboxylate
C19 H18 N2 O5
GGBHINRNYAAYMX-INIZCTEOSA-N
NAG

Query on NAG



Download:Ideal Coordinates CCD File
BA [auth B]
CA [auth B]
DA [auth B]
EA [auth B]
FA [auth B]
BA [auth B],
CA [auth B],
DA [auth B],
EA [auth B],
FA [auth B],
Q [auth A],
R [auth A],
S [auth A],
T [auth A],
U [auth A],
V [auth A]
2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
PEG

Query on PEG



Download:Ideal Coordinates CCD File
W [auth A]DI(HYDROXYETHYL)ETHER
C4 H10 O3
MTHSVFCYNBDYFN-UHFFFAOYSA-N
GLY

Query on GLY



Download:Ideal Coordinates CCD File
GA [auth B],
IA [auth B],
Y [auth A],
Z [auth A]
GLYCINE
C2 H5 N O2
DHMQDGOQFOQNFH-UHFFFAOYSA-N
ZN

Query on ZN



Download:Ideal Coordinates CCD File
AA [auth B],
O [auth A]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
EDO

Query on EDO



Download:Ideal Coordinates CCD File
HA [auth B],
X [auth A]
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.03 Å
  • R-Value Free:  0.242 (Depositor), 0.245 (DCC) 
  • R-Value Work:  0.203 (Depositor), 0.203 (DCC) 
  • R-Value Observed: 0.205 (Depositor) 
Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 68.377α = 90
b = 257.679β = 110.444
c = 73.494γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
PHENIXrefinement
XDSdata reduction
STARANISOdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
European Union (EU)European Union--

Revision History  (Full details and data files)

  • Version 1.0: 2024-01-31
    Type: Initial release
  • Version 1.1: 2024-02-14
    Changes: Database references
  • Version 1.2: 2024-10-23
    Changes: Structure summary