4PES

Crystal structure of insulin degrading enzyme complexed with inhibitor tert-butyl [(2S)-2-(2,5-difluorophenyl)-3-(quinolin-3-yl)propyl]carbamate

• PDB DOI: https://doi.org/10.2210/pdb4PES/pdb

• Classification: HYDROLASE/HYDROLASE INHIBITOR
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2014-04-24 Released: 2015-06-17 
• Deposition Author(s): Wang, Y., Guo, S.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.21 Å
• R-Value Free: 0.256 
• R-Value Work: 0.209 
• R-Value Observed: 0.209 

Literature

Crystal structure of IDE complexed with an inhibitor

Durham, T.B., Toth, J.L., Klimkowski, V.J., Cao, J.X.C., Siesky, A.M., Alexander-Chacko, J., Wu, G.Y., Dixon, J.T., McGee, J.E., Wang, Y., Guo, S., Cavitt, R.N., Schindler, J., Thibodeaux, S.J., Calvert, N.A., Coghlan, M.J., Sindelar, D.K., Christe, M., Kiselyov, V.V., Dodson, M., Sloop, K.W.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 230.38 kDa 
• Atom Count: 16,206 
• Modelled Residue Count: 1,920 
• Deposited Residue Count: 1,984 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Insulin-degrading enzyme	A, B	989	Homo sapiens	Mutation(s): 14  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 ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Ala-Ala-Ala	C, D	3	Homo sapiens	Mutation(s): 0

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
2PJ	E [auth A], G [auth B]	tert-butyl [(2S)-2-(2,5-difluorophenyl)-3-(quinolin-3-yl)propyl]carbamate C23 H24 F2 N2 O2 IRFHMTUHTBSEBK-QGZVFWFLSA-N
ZN	F [auth A], H [auth B]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.21 Å
• R-Value Free: 0.256 
• R-Value Work: 0.209 
• R-Value Observed: 0.209 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 78.754	α = 90
b = 116.087	β = 98.09
c = 123.923	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
SCALA	data scaling
MOSFLM	data reduction
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2015-06-17 
Deposition Author(s): Wang, Y., Guo, S.

Revision History  

• Version 1.0: 2015-06-17
  Type: Initial release
  
• Version 2.0: 2023-09-27
  Changes: Data collection, Database references, Derived calculations, Non-polymer description, Other, Refinement description, Source and taxonomy, Structure summary