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 

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This is version 1.4 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: https://doi.org/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, which is mediated primarily by insulin-degrading enzyme (IDE), a structurally and evolutionarily distinctive zinc-metalloprotease ...

    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)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Insulin-degrading enzyme
A, B
1,019Homo sapiensMutation(s): 20 
Gene Names: IDE
EC: 3.4.24.56
UniProt & NIH Common Fund Data Resources
Find proteins for P14735 (Homo sapiens)
Explore P14735 
Go to UniProtKB:  P14735
PHAROS:  P14735
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP14735
Protein Feature View
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  • Reference Sequence

Find similar proteins by:  Sequence   |   3D Structure  

Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
HYDROXAMATE PEPTIDE II1C [auth F],
D [auth G]		3synthetic 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 Ideal Coordinates CCD File 
F [auth A],
R [auth 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
Download Ideal Coordinates CCD File 
G [auth A]
H [auth A]
S [auth B]
T [auth B]
U [auth B]
G [auth A],
H [auth A],
S [auth B],
T [auth B],
U [auth B],
V [auth B],
W [auth B]
1,4-DIETHYLENE DIOXIDE
C4 H8 O2
RYHBNJHYFVUHQT-UHFFFAOYSA-N		 Ligand Interaction
ZN
Query on ZN
Download Ideal Coordinates CCD File 
E [auth A],
Q [auth B]		ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N		 Ligand Interaction
ACY
Query on ACY
Download Ideal Coordinates CCD File 
AA [auth B]
BA [auth B]
CA [auth B]
I [auth A]
J [auth A]
AA [auth B],
BA [auth B],
CA [auth B],
I [auth A],
J [auth A],
K [auth A],
L [auth A],
M [auth A],
N [auth A],
O [auth A],
P [auth A],
X [auth B],
Y [auth B],
Z [auth B]
ACETIC ACID
C2 H4 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-N		 Ligand Interaction
Binding Affinity Annotations 
IDSourceBinding Affinity
QIX PDBBind:  3E4A Ki: 1.7 (nM) from 1 assay(s)
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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Ligand Structure Quality Assessment 


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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • 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
  • Version 1.3: 2021-10-20
    Changes: Database references, Derived calculations
  • Version 1.4: 2023-08-30
    Changes: Data collection, Refinement description