3E4A

Human IDE-inhibitor complex at 2.6 angstrom resolution


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.60 Å
  • R-Value Free: 0.225 
  • R-Value Work: 0.167 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Designed inhibitors of insulin-degrading enzyme regulate the catabolism and activity of insulin.

Leissring, M.A.Malito, E.Hedouin, S.Reinstatler, L.Sahara, T.Abdul-Hay, S.O.Choudhry, S.Maharvi, G.M.Fauq, A.H.Huzarska, M.May, P.S.Choi, S.Logan, T.P.Turk, B.E.Cantley, L.C.Manolopoulou, M.Tang, W.J.Stein, R.L.Cuny, G.D.Selkoe, D.J.

(2010) PLoS One 5: e10504-e10504

  • DOI: 10.1371/journal.pone.0010504
  • Primary Citation of Related Structures:  
    3E4A

  • PubMed Abstract: 
  • Insulin is a vital peptide hormone that is a central regulator of glucose homeostasis, and impairments in insulin signaling cause diabetes mellitus. In principle, it should be possible to enhance the activity of insulin by inhibiting its catabolism, ...

    Insulin is a vital peptide hormone that is a central regulator of glucose homeostasis, and impairments in insulin signaling cause diabetes mellitus. In principle, it should be possible to enhance the activity of insulin by inhibiting its catabolism, which is mediated primarily by insulin-degrading enzyme (IDE), a structurally and evolutionarily distinctive zinc-metalloprotease. Despite interest in pharmacological inhibition of IDE as an attractive anti-diabetic approach dating to the 1950s, potent and selective inhibitors of IDE have not yet emerged.


    Organizational Affiliation

    Department of Neuroscience, Mayo Clinic Florida, Jacksonville, Florida, United States of America. Leissring@mayo.edu



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Insulin-degrading enzymeAB1019Homo sapiensMutation(s): 20 
Gene Names: IDE
EC: 3.4.24.56
Find proteins for P14735 (Homo sapiens)
Explore P14735 
Go to UniProtKB:  P14735
NIH Common Fund Data Resources
PHAROS  P14735
Protein Feature View
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  • Reference Sequence
  • Find similar proteins by:  Sequence   |   Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
HYDROXAMATE PEPTIDE II1FG3synthetic constructMutation(s): 0 
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
QIX
Query on QIX

Download CCD File 
A, B
N~2~-[(2R)-4-(HYDROXYAMINO)-2-(2-NAPHTHYLMETHYL)-4-OXOBUTANOYL]-L-ARGINYLGLYCYLGLYCINAMIDE
C25 H34 N8 O6
NINUSDCYEXCHSI-MOPGFXCFSA-N
 Ligand Interaction
DIO
Query on DIO

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A, B
1,4-DIETHYLENE DIOXIDE
C4 H8 O2
RYHBNJHYFVUHQT-UHFFFAOYSA-N
 Ligand Interaction
ZN
Query on ZN

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

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A, B
ACETIC ACID
C2 H4 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
QIXKi :  1.7000000476837158   nM  PDBBind
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.60 Å
  • R-Value Free: 0.225 
  • R-Value Work: 0.167 
  • Space Group: P 65
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 261.402α = 90
b = 261.402β = 90
c = 92.054γ = 120
Software Package:
Software NamePurpose
PHASERphasing
PHENIXrefinement
SBC-Collectdata collection
HKL-2000data reduction
SCALEPACKdata scaling

Structure Validation

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Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2009-05-19
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2017-10-25
    Changes: Refinement description, Source and taxonomy