2B8L

Crystal structure of human beta secretase complexed with inhibitor

• PDB DOI: https://doi.org/10.2210/pdb2B8L/pdb

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


• Deposited: 2005-10-07 Released: 2005-10-18 
• Deposition Author(s): Munshi, S.K., Kuo, L.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free: 0.252 
• R-Value Work: 0.220 
• R-Value Observed: 0.230 

Starting Model: experimental

Literature

Conformationally biased P3 amide replacements of beta-secretase inhibitors

Stachel, S.J., Coburn, C.A., Steele, T.G., Crouthamel, M.C., Pietrak, B.L., Lai, M.T., Holloway, M.K., Munshi, S.K., Graham, S.L., Vacca, J.P.

(2006) Bioorg Med Chem Lett 16: 641-644

• PubMed: 16263281 
• DOI: https://doi.org/10.1016/j.bmcl.2005.10.032
• Primary Citation of Related Structures:  
  2B8L, 2B8V


• PubMed Abstract: 
  

  We have synthesized and evaluated a series of conformationally biased P3 amide replacements based on an isophthalamide lead structure. The studies resulted in the identification of the beta-secretase inhibitor 7m which has an in vitro IC(50)=35 nM. The synthesis and biological activities of these compounds are described.

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Organizational Affiliation: 

Department of Medicinal Chemistry, Merck Research Laboratories, 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: 45.7 kDa 
• Atom Count: 3,221 
• Modelled Residue Count: 379 
• Deposited Residue Count: 405 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Beta-secretase 1	A	405	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) Go to UniProtKB:  P56817
PHAROS:  P56817 GTEx:  ENSG00000186318

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
5HA	B [auth A]	N-[(1S,2R)-1-BENZYL-3-(CYCLOPROPYLAMINO)-2-HYDROXYPROPYL]-5-[METHYL(METHYLSULFONYL)AMINO]-N'-[(1R)-1-PHENYLETHYL]ISOPHTHALAMIDE C31 H38 N4 O5 S VPNIQGRFZCTBEZ-SPTGULJVSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
5HA	BindingDB:  2B8L	Ki: 233 (nM) from 1 assay(s)
		IC50: min: 10, max: 1.50e+4 (nM) from 13 assay(s)
		EC50: 43 (nM) from 1 assay(s)
	PDBBind:  2B8L	IC50: 15 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free: 0.252 
• R-Value Work: 0.220 
• R-Value Observed: 0.230 
• Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 104.678	α = 90
b = 127.917	β = 90
c = 76.122	γ = 90

Software Package:

Software Name	Purpose
HKL-2000	data collection
SCALEPACK	data scaling
CNX	refinement
HKL-2000	data reduction
CNX	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2005-10-18 
Deposition Author(s): Munshi, S.K., Kuo, L.

Revision History  

• Version 1.0: 2005-10-18
  Type: Initial release
  
• Version 1.1: 2007-10-11
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2021-10-20
  Changes: Database references, Derived calculations
• Version 1.4: 2023-08-23
  Changes: Data collection, Refinement description
• Version 1.5: 2024-10-30
  Changes: Structure summary