7K1E

Crystal structure of human insulin degrading enzyme (IDE) in complex with compound BDM_88646


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free: 0.209 
  • R-Value Work: 0.158 
  • R-Value Observed: 0.159 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history


Literature

Crystal structure of human insulin degrading enzyme (IDE) in complex with compound 3

Liang, W.G.Deprez, R.Bosc, D.Tang, W.

To be published.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Insulin-degrading enzyme
A, B
990Homo sapiensMutation(s): 13 
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
GTEx:  ENSG00000119912 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP14735
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
VQG (Subject of Investigation/LOI)
Query on VQG

Download Ideal Coordinates CCD File 
D [auth A],
J [auth B]
3,4-difluoro-N-[(1S)-1-{1-[(2R)-4-(hydroxyamino)-4-oxo-1-(5,6,7,8-tetrahydronaphthalen-2-yl)butan-2-yl]-1H-1,2,3-triazol-4-yl}ethyl]benzamide
C25 H27 F2 N5 O3
VQGQRXDQPMXXSZ-MGPUTAFESA-N
EPE
Query on EPE

Download Ideal Coordinates CCD File 
H [auth A],
N [auth B]
4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID
C8 H18 N2 O4 S
JKMHFZQWWAIEOD-UHFFFAOYSA-N
DIO
Query on DIO

Download Ideal Coordinates CCD File 
E [auth A]
F [auth A]
G [auth A]
K [auth B]
L [auth B]
E [auth A],
F [auth A],
G [auth A],
K [auth B],
L [auth B],
M [auth B]
1,4-DIETHYLENE DIOXIDE
C4 H8 O2
RYHBNJHYFVUHQT-UHFFFAOYSA-N
ZN
Query on ZN

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

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free: 0.209 
  • R-Value Work: 0.158 
  • R-Value Observed: 0.159 
  • Space Group: P 65
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 267.88α = 90
b = 267.88β = 90
c = 89.611γ = 120
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-3000data reduction
HKL-3000data scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of Mental Health (NIH/NIMH)United StatesR01 GM121964

Revision History  (Full details and data files)

  • Version 1.0: 2021-09-22
    Type: Initial release
  • Version 1.1: 2023-10-18
    Changes: Data collection, Refinement description