Macromolecule Content

Total Structure Weight: 230.05 kDa
Atom Count: 15726
Modelled Residue Count: 1908
Deposited Residue Count: 1980
Unique protein chains: 1

4GS8

Structure analysis of cysteine free insulin degrading enzyme (ide) with compound bdm43079 [{[(s)-2-(1h-imidazol-4-yl)-1-methylcarbamoyl-ethylcarbamoyl]-methyl}-(3-phenyl-propyl)-amino]-acetic acid

DOI: 10.2210/pdb4GS8/pdb

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

Deposited: 2012-08-27 Released: 2013-08-28
Deposition Author(s): Guo, Q., Deprez-Poulain, R., Deprez, B., Tang, W.J.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.99 Å
R-Value Free: 0.235
R-Value Work: 0.178
R-Value Observed: 0.181

wwPDB Validation 3D Report Full Report

This is version 1.2 of the entry. See complete history.

Literature

Imidazole-derived 2-[N-carbamoylmethyl-alkylamino]acetic acids, substrate-dependent modulators of insulin-degrading enzyme in amyloid-beta hydrolysis.

Charton, J., Gauriot, M., Guo, Q., Hennuyer, N., Marechal, X., Dumont, J., Hamdane, M., Pottiez, V., Landry, V., Sperandio, O., Flipo, M., Buee, L., Staels, B., Leroux, F., Tang, W.J., Deprez, B., Deprez-Poulain, R.

(2014) Eur J Med Chem 79: 184-193

PubMed: 24735644 Search on PubMedSearch on PubMed Central
DOI: 10.1016/j.ejmech.2014.04.009
Primary Citation of Related Structures:
4DTT, 4DWK, 4GS8, 4GSC, 3QZ2, 2YPU

PubMed Abstract:

Macromolecules

Find similar proteins by:

(by identity cutoff) | Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Insulin-degrading enzyme	A, B	990	Homo sapiens	Mutation(s): 14 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 GTEx: ENSG00000119912
Protein Feature View Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
MGJ Query on MGJ Download Ideal Coordinates CCD File SDF format, chain C [A] SDF format, chain E [B] MOL2 format, chain C [A] MOL2 format, chain E [B]	A, B	N-(carboxymethyl)-N-(3-phenylpropyl)glycyl-N-methyl-L-histidinamide C₂₀ H₂₇ N₅ O₄ QEPAXTJXHXPFJN-KRWDZBQOSA-N		Ligand Interaction
ZN Query on ZN Download Ideal Coordinates CCD File SDF format, chain D [A] SDF format, chain F [B] MOL2 format, chain D [A] MOL2 format, chain F [B]	A, B	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Ligand Interaction

External Ligand Annotations
ID	Binding Affinity (Sequence Identity %)
MGJ	IC50: 100 nM BindingDB
MGJ	EC50: 530 nM BindingDB
MGJ	IC50: 3100 nM BindingDB

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.99 Å
R-Value Free: 0.235
R-Value Work: 0.178
R-Value Observed: 0.181
Space Group: P 6₅

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 263.553	α = 90
b = 263.553	β = 90
c = 91.095	γ = 120

Software Package:

Software Name	Purpose
HKL-3000	data collection
PHASES	phasing
REFMAC	refinement
HKL-3000	data reduction
HKL-3000	data scaling

Structure Validation

View Full Validation Report

Entry History

Deposition Data

Deposited Date: 2012-08-27
Released Date: 2013-08-28

Deposition Author(s):

Deprez-Poulain, R.

Revision History (Full details and data files)

Version 1.0: 2013-08-28
Type: Initial release
Version 1.1: 2014-04-16
Changes: Database references
Version 1.2: 2014-05-28
Changes: Database references

RCSB PDB is funded by the National Science Foundation (DBI-1832184), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM133198.