6YDX

Insulin-regulated aminopeptidase complexed with a macrocyclic peptidic inhibitor


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.20 Å
  • R-Value Free: 0.314 
  • R-Value Work: 0.277 
  • R-Value Observed: 0.277 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 2.1 of the entry. See complete history


Literature

Structural Basis of Inhibition of Insulin-Regulated Aminopeptidase by a Macrocyclic Peptidic Inhibitor.

Mpakali, A.Saridakis, E.Giastas, P.Maben, Z.Stern, L.J.Larhed, M.Hallberg, M.Stratikos, E.

(2020) ACS Med Chem Lett 11: 1429-1434

  • DOI: https://doi.org/10.1021/acsmedchemlett.0c00172
  • Primary Citation of Related Structures:  
    6YDX

  • PubMed Abstract: 

    Insulin-regulated aminopeptidase (IRAP) is a transmembrane zinc metallopeptidase with many important biological functions and an emerging pharmacological target. Although previous structural studies have given insight on how IRAP recognizes linear peptides, how it recognizes its physiological cyclic ligands remains elusive. Here, we report the first crystal structure of IRAP with the macrocyclic peptide inhibitor HA08 that combines structural elements from angiotensin IV and the physiological substrates oxytocin and vasopressin. The compound is found in the catalytic site in a near canonical substrate-like configuration and inhibits by a competitive mechanism. Comparison with previously solved structures of IRAP along with small-angle X-ray scattering experiments suggests that IRAP is in an open conformation in solution but undergoes a closing conformational change upon inhibitor binding. Stabilization of the closed conformation in combination with catalytic water exclusion by the tightly juxtaposed GAMEN loop is proposed as a mechanism of inhibition.


  • Organizational Affiliation

    National Center for Scientific Research Demokritos, Agia Paraskevi, Athens 15341, Greece.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Leucyl-cystinyl aminopeptidase
A, B
912Homo 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: 9Go to GlyGen: Q9UIQ6-1
Sequence Annotations
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  • Reference Sequence
Oligosaccharides

Help

Entity ID: 2
MoleculeChains Length2D Diagram Glycosylation3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
C, E, F, G, I
2N-Glycosylation
Glycosylation Resources
GlyTouCan:  G42666HT
GlyCosmos:  G42666HT
GlyGen:  G42666HT
Entity ID: 3
MoleculeChains Length2D Diagram Glycosylation3D Interactions
beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
D, H
3N-Glycosylation
Glycosylation Resources
GlyTouCan:  G15407YE
GlyCosmos:  G15407YE
GlyGen:  G15407YE
Small Molecules
Ligands 9 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
ONN (Subject of Investigation/LOI)
Query on ONN

Download Ideal Coordinates CCD File 
J [auth A],
W [auth B]
2-[2-[[[(4~{R},8~{S},11~{S})-11-azanyl-8-[(4-hydroxyphenyl)methyl]-6,10-bis(oxidanylidene)-1,2-dithia-5,9-diazacyclotridec-4-yl]carbonylamino]methyl]phenyl]ethanoic acid
C26 H32 N4 O6 S2
VZYRMNZEFCZSER-BVSLBCMMSA-N
NAG
Query on NAG

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AA [auth B]
BA [auth B]
CA [auth B]
L [auth A]
M [auth A]
AA [auth B],
BA [auth B],
CA [auth B],
L [auth A],
M [auth A],
N [auth A],
O [auth A],
P [auth A],
Y [auth B],
Z [auth B]
2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
PG4
Query on PG4

Download Ideal Coordinates CCD File 
U [auth A]TETRAETHYLENE GLYCOL
C8 H18 O5
UWHCKJMYHZGTIT-UHFFFAOYSA-N
PGE
Query on PGE

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T [auth A]TRIETHYLENE GLYCOL
C6 H14 O4
ZIBGPFATKBEMQZ-UHFFFAOYSA-N
SIN
Query on SIN

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Q [auth A]SUCCINIC ACID
C4 H6 O4
KDYFGRWQOYBRFD-UHFFFAOYSA-N
PEG
Query on PEG

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GA [auth B]DI(HYDROXYETHYL)ETHER
C4 H10 O3
MTHSVFCYNBDYFN-UHFFFAOYSA-N
PO4
Query on PO4

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V [auth A]PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
ZN
Query on ZN

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K [auth A],
X [auth B]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
EDO
Query on EDO

Download Ideal Coordinates CCD File 
DA [auth B],
EA [auth B],
FA [auth B],
R [auth A],
S [auth A]
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
Binding Affinity Annotations 
IDSourceBinding Affinity
ONN BindingDB:  6YDX Ki: min: 3.3, max: 1265 (nM) from 3 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.20 Å
  • R-Value Free: 0.314 
  • R-Value Work: 0.277 
  • R-Value Observed: 0.277 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 73.419α = 90
b = 118.631β = 102.767
c = 141.389γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XDSdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
European CommissionEuropean UnioniNEXT 5589
General Secretariat for Research and Technology (GSRT)GreeceINSPIRED MIS 5002550

Revision History  (Full details and data files)

  • Version 1.0: 2020-07-22
    Type: Initial release
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Atomic model, Data collection, Database references, Derived calculations, Structure summary
  • Version 2.1: 2024-01-24
    Changes: Data collection, Database references, Refinement description