2PH8

Crystal Structure of Human Beta Secretase Complexed with inhibitor

• PDB DOI: https://doi.org/10.2210/pdb2PH8/pdb

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


• Deposited: 2007-04-10 Released: 2008-04-22 
• Deposition Author(s): Munshi, S.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free: 0.204 
• R-Value Work: 0.185 
• R-Value Observed: 0.186 

Starting Model: experimental

Literature

Strategies toward improving the brain penetration of macrocyclic tertiary carbinamine BACE-1 inhibitors.

Moore, K.P., Zhu, H., Rajapakse, H.A., McGaughey, G.B., Colussi, D., Price, E.A., Sankaranarayanan, S., Simon, A.J., Pudvah, N.T., Hochman, J.H., Allison, T., Munshi, S.K., Graham, S.L., Vacca, J.P., Nantermet, P.G.

(2007) Bioorg Med Chem Lett 17: 5831-5835

• PubMed: 17827011 
• DOI: https://doi.org/10.1016/j.bmcl.2007.08.040
• Primary Citation of Related Structures:  
  2PH8, 2QZK


• PubMed Abstract: 
  

  This letter describes replacements for the P3 amide moiety present in previously reported tertiary carbinamine macrolactones. Although P-gp efflux issues associated with these amide-macrolactones were solved and full brain penetration was measured in one case, potency was compromised in the process.

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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: 45.77 kDa 
• Atom Count: 3,206 
• Modelled Residue Count: 365 
• 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) Explore P56817  Go to UniProtKB:  P56817
PHAROS:  P56817 GTEx:  ENSG00000186318

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
35A	D [auth A]	N-[(5R,14R)-5-AMINO-5,14-DIMETHYL-4-OXO-3-OXA-18-AZATRICYCLO[15.3.1.1~7,11~]DOCOSA-1(21),7(22),8,10,17,19-HEXAEN-19-YL]-N-METHYLMETHANESULFONAMIDE C24 H33 N3 O4 S QWDOKZPZLWNULU-MZNJEOGPSA-N
SO4	B [auth A], C [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Binding Affinity Annotations
ID	Source	Binding Affinity
35A	PDBBind:  2PH8	IC50: 1800 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free: 0.204 
• R-Value Work: 0.185 
• R-Value Observed: 0.186 
• Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 103.811	α = 90
b = 128.523	β = 90
c = 76.276	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	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