2P8H

Crystal structure of human beta secretase complexed with inhibitor

• PDB DOI: https://doi.org/10.2210/pdb2P8H/pdb

• Classification: HYDROLASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2007-03-22 Released: 2007-08-14 
• Deposition Author(s): Munshi, S.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 0.249 
• R-Value Work: 0.221 
• R-Value Observed: 0.224 

Starting Model: experimental

Literature

Design and Synthesis of 2,3,5-Substituted Imidazolidin-4-one Inhibitors of BACE-1.

Barrow, J.C., Rittle, K.E., Ngo, P.L., Selnick, H.G., Graham, S.L., Pitzenberger, S.M., McGaughey, G.B., Colussi, D., Lai, M.T., Huang, Q., Tugusheva, K., Espeseth, A.S., Simon, A.J., Munshi, S.K., Vacca, J.P.

(2007) ChemMedChem 2: 995-999

• PubMed: 17458843 
• DOI: https://doi.org/10.1002/cmdc.200700038
• Primary Citation of Related Structures:  
  2P8H

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Organizational Affiliation: 

Department of Medicinal Chemistry, Merck Research Laboratories, P.O Box 4, WP14-1, 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: 45.78 kDa 
• Atom Count: 3,291 
• 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): 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
MY9	B [auth A]	N-{(1S,2S)-1-BENZYL-2-HYDROXY-2-[(4S)-1,2,2-TRIMETHYL-5-OXOIMIDAZOLIDIN-4-YL]ETHYL}-N'-[(1R)-1-(4-FLUOROPHENYL)ETHYL]-5-[METHYL(METHYLSULFONYL)AMINO]ISOPHTHALAMIDE C33 H40 F N5 O6 S YNXGIROKYOHHJW-UFAZYNLISA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
MY9	PDBBind:  2P8H	IC50: 71 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 0.249 
• R-Value Work: 0.221 
• R-Value Observed: 0.224 
• Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 104.569	α = 90
b = 127.291	β = 90
c = 76.085	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2007-08-14 
Deposition Author(s): Munshi, S.

Revision History  

• Version 1.0: 2007-08-14
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2023-08-30
  Changes: Data collection, Database references, Refinement description