7K1F

Crystal structure of human insulin degrading enzyme (IDE) in complex with compound BDM_88558


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.60 Å
  • R-Value Free: 0.208 
  • R-Value Work: 0.170 
  • R-Value Observed: 0.170 

wwPDB Validation   3D Report Full Report


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 4

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
Expand
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
VQJ (Subject of Investigation/LOI)
Query on VQJ

Download Ideal Coordinates CCD File 
D [auth A],
J [auth B]
3,4-difluoro-N-({1-[(2R)-4-(hydroxyamino)-4-oxo-1-(quinolin-7-yl)butan-2-yl]-1H-1,2,3-triazol-4-yl}methyl)benzamide
C23 H20 F2 N6 O3
NEONSMDVMOADLB-GOSISDBHSA-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: 2.60 Å
  • R-Value Free: 0.208 
  • R-Value Work: 0.170 
  • R-Value Observed: 0.170 
  • Space Group: P 65
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 265.54α = 90
b = 265.54β = 90
c = 90.057γ = 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