2QZL

Crystal Structure of human Beta Secretase complexed with IXS

• PDB DOI: https://doi.org/10.2210/pdb2QZL/pdb

• Classification: HYDROLASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): Yes 


• Deposited: 2007-08-16 Released: 2008-04-22 
• Deposition Author(s): Munshi, S.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 0.241 
• R-Value Work: 0.216 
• R-Value Observed: 0.217 

Starting Model: experimental

Literature

BACE-1 inhibition by a series of psi[CH2NH] reduced amide isosteres

Coburn, C.A., Stachel, S.J., Jones, K.G., Steele, T.G., Rush, D.M., DiMuzio, J., Pietrak, B.L., Lai, M.T., Huang, Q., Lineberger, J., Jin, L., Munshi, S., Holloway, K.M., Espeseth, A., Simon, A., Hazuda, D., Graham, S.L., Vacca, J.P.

(2006) Bioorg Med Chem Lett 16: 3635-3638

• PubMed: 16690314 
• DOI: https://doi.org/10.1016/j.bmcl.2006.04.076
• Primary Citation of Related Structures:  
  2QZL


• PubMed Abstract: 
  

  A series of beta-site amyloid precursor protein cleaving enzyme (BACE-1) inhibitors containing a psi(CH2NH) reduced amide bond were synthesized. Incorporation of this reduced amide isostere as a non-cleavable peptide surrogate afforded inhibitors possessing low nanomolar potencies in both an enzymatic and cell-based assay.

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Organizational Affiliation: 

Department of Medicinal Chemistry, Merck Research Laboratories, PO Box 4, West Point, PA 19486, USA. [e-mail]

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 46.45 kDa 
• Atom Count: 3,418 
• Modelled Residue Count: 375 
• Deposited Residue Count: 411 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Beta-secretase 1	A	411	Homo sapiens	Mutation(s): 2  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
IXS	B [auth A]	N-[(1S)-1-benzyl-2-{[(1S)-2-(isobutylamino)-1-methyl-2-oxoethyl]amino}ethyl]-N'-[(1R)-1-(4-fluorophenyl)ethyl]-5-[methyl(methylsulfonyl)amino]isophthalamide C34 H44 F N5 O5 S FZTXBRKPIRTQCY-QEGDFHJFSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
IXS	BindingDB:  2QZL	IC50: 8 (nM) from 1 assay(s)
	PDBBind:  2QZL	IC50: 8 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 0.241 
• R-Value Work: 0.216 
• R-Value Observed: 0.217 
• Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 104.931	α = 90
b = 128.152	β = 90
c = 76.307	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
d*TREK	data reduction
d*TREK	data scaling
REFMAC	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2008-04-22 
Deposition Author(s): Munshi, S.

Revision History  

• Version 1.0: 2008-04-22
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2021-10-20
  Changes: Database references, Derived calculations
• Version 1.3: 2023-08-30
  Changes: Data collection, Refinement description
• Version 1.4: 2024-10-09
  Changes: Structure summary