3EXO

Crystal structure of BACE1 bound to inhibitor

• PDB DOI: https://doi.org/10.2210/pdb3EXO/pdb

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


• Deposited: 2008-10-16 Released: 2009-02-03 
• Deposition Author(s): Allison, T.J.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free: 0.295 
• R-Value Work: 0.229 
• R-Value Observed: 0.232 

Literature

Identification of a small molecule beta-secretase inhibitor that binds without catalytic aspartate engagement.

Steele, T.G., Hills, I.D., Nomland, A.A., de Leon, P., Allison, T., McGaughey, G., Colussi, D., Tugusheva, K., Haugabook, S.J., Espeseth, A.S., Zuck, P., Graham, S.L., Stachel, S.J.

(2009) Bioorg Med Chem Lett 19: 17-20

• PubMed: 19036583 
• DOI: https://doi.org/10.1016/j.bmcl.2008.11.027
• Primary Citation of Related Structures:  
  3EXO


• PubMed Abstract: 
  

  A small molecule inhibitor of beta-secretase with a unique binding mode has been developed. Crystallographic determination of the enzyme-inhibitor complex shows the catalytic aspartate residues in the active site are not engaged in inhibitor binding. This unprecedented binding mode in the field of aspartyl protease inhibition is described.

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Organizational Affiliation: 

Department of Medicinal Chemistry, Merck Research Laboratories, Merck & Co, West Point, PA 19486, USA.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 46.73 kDa 
• Atom Count: 3,389 
• Modelled Residue Count: 373 
• Deposited Residue Count: 413 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Beta-secretase 1	A	413	Homo sapiens	Mutation(s): 2  Gene Names: BACE1, BACE, KIAA1149 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 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
5MS	F [auth A]	N-{2-methyl-5-[(6-phenylpyrimidin-4-yl)amino]phenyl}methanesulfonamide C18 H18 N4 O2 S CXQRKICWSCAUGW-UHFFFAOYSA-N
SO4	B [auth A], C [auth A], D [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
GOL	E [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
5MS	BindingDB:  3EXO	IC50: 2.40e+4 (nM) from 1 assay(s)
	PDBBind:  3EXO	IC50: 2.40e+4 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free: 0.295 
• R-Value Work: 0.229 
• R-Value Observed: 0.232 
• Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 104.433	α = 90
b = 127.923	β = 90
c = 76.671	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
StructureStudio	data collection
MOLREP	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2009-02-03 
Deposition Author(s): Allison, T.J.

Revision History  

• Version 1.0: 2009-02-03
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Non-polymer description, Version format compliance
• Version 1.2: 2017-10-25
  Changes: Refinement description
• Version 1.3: 2021-10-20
  Changes: Database references, Derived calculations
• Version 1.4: 2023-12-27
  Changes: Data collection
• Version 1.5: 2024-10-09
  Changes: Structure summary