2IQG

Crystal Structure of Hydroxyethyl Secondary Amine-based Peptidomimetic Inhibitor of Human Beta-Secretase (BACE)

• PDB DOI: https://doi.org/10.2210/pdb2IQG/pdb

• Classification: HYDROLASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2006-10-13 Released: 2007-02-27 
• Deposition Author(s): Benson, T.E., Woods, D.D., Prince, D.B., Tomasselli, A.G., Emmons, T.L.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free: 0.231 
• R-Value Work: 0.206 

Literature

Design, Synthesis, and Crystal Structure of Hydroxyethyl Secondary Amine-Based Peptidomimetic Inhibitors of Human beta-Secretase.

Maillard, M.C., Hom, R.K., Benson, T.E., Moon, J.B., Mamo, S., Bienkowski, M., Tomasselli, A.G., Woods, D.D., Prince, D.B., Paddock, D.J., Emmons, T.L., Tucker, J.A., Dappen, M.S., Brogley, L., Thorsett, E.D., Jewett, N., Sinha, S., John, V.

(2007) J Med Chem 50: 776-781

• PubMed: 17300163 
• DOI: https://doi.org/10.1021/jm061242y
• Primary Citation of Related Structures:  
  2IQG


• PubMed Abstract: 
  

  The design and synthesis of a novel series of potent and cell permeable peptidomimetic inhibitors of the human beta-secretase (BACE) are described. These inhibitors feature a hydroxyethyl secondary amine isostere and a novel aromatic ring replacement for the C-terminus. The crystal structure of BACE in complex with this hydroxyethyl secondary amine isostere inhibitor is also presented.

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Organizational Affiliation: 

Elan Pharmaceuticals, 800 Gateway Boulevard, South San Francisco, California 94080, USA.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 46.12 kDa 
• Atom Count: 3,393 
• Modelled Residue Count: 375 
• Deposited Residue Count: 406 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Beta-secretase 1	A	406	Homo sapiens	Mutation(s): 0  Gene Names: BACE1, BACE EC: 3.4.23.46
UniProt & NIH Common Fund Data Resources
Find proteins for P56817 (Homo sapiens) Explore P56817  Go to UniProtKB:  P56817
PHAROS:  P56817 GTEx:  ENSG00000186318

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
F2I	B [auth A]	N'-{(1S,2R)-1-(3,5-DIFLUOROBENZYL)-2-HYDROXY-3-[(3-IODOBENZYL)AMINO]PROPYL}-5-METHYL-N,N-DIPROPYLISOPHTHALAMIDE C32 H38 F2 I N3 O3 FSQSHDXWJKXBPP-XZWHSSHBSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
F2I	PDBBind:  2IQG	IC50: 5 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free: 0.231 
• R-Value Work: 0.206 
• Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 73.09	α = 90
b = 105.08	β = 94.81
c = 50.5	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
CNS	refinement
PDB_EXTRACT	data extraction
HKL-2000	data reduction
X-PLOR	refinement

Structure Validation

Entry History 

Deposition Data

• Released Date: 2007-02-27 
Deposition Author(s): Benson, T.E., Woods, D.D., Prince, D.B., Tomasselli, A.G., Emmons, T.L.

Revision History  

• Version 1.0: 2007-02-27
  Type: Initial release
  
• Version 1.1: 2008-05-01
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2017-10-18
  Changes: Refinement description
• Version 1.4: 2024-10-16
  Changes: Data collection, Database references, Structure summary