2HIZ

Crystal Structure of human beta-secretase (BACE) in the presence of an inhibitor

• PDB DOI: https://doi.org/10.2210/pdb2HIZ/pdb

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


• Deposited: 2006-06-29 Released: 2007-01-23 
• Deposition Author(s): Benson, T.E., Prince, D.B., Tomasselli, A.G., Emmons, T.L., Paddock, D.J.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free: 
  0.253 (Depositor), 0.243 (DCC) 
• R-Value Work: 
  0.214 (Depositor), 0.206 (DCC) 

Literature

Design of potent inhibitors of human beta-secretase. Part 1.

Freskos, J.N., Fobian, Y.M., Benson, T.E., Bienkowski, M.J., Brown, D.L., Emmons, T.L., Heintz, R., Laborde, A., McDonald, J.J., Mischke, B.V., Molyneaux, J.M., Moon, J.B., Mullins, P.B., Bryan Prince, D., Paddock, D.J., Tomasselli, A.G., Winterrowd, G.

(2007) Bioorg Med Chem Lett 17: 73-77

• PubMed: 17046251 
• DOI: https://doi.org/10.1016/j.bmcl.2006.09.092
• Primary Citation of Related Structures:  
  2HIZ


• PubMed Abstract: 
  

  We describe a novel series of potent inhibitors of human beta-secretase. These compounds possess the hydroxyethyl amine transition state isostere. A 2.5A crystal structure of inhibitor 32 bound to BACE is provided.

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Organizational Affiliation: 

Pfizer Inc., 700N. Chesterfield Pkwy., St. Louis, MO 63198, USA. [e-mail]

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly 2  

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

Biological assembly 2 assigned by authors.

Biological Assembly 3  

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

Biological assembly 3 assigned by authors.

Macromolecule Content

• Total Structure Weight: 153.04 kDa 
• Atom Count: 9,176 
• Modelled Residue Count: 1,116 
• Deposited Residue Count: 1,365 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Beta-secretase 1	A, B, C	455	Homo sapiens	Mutation(s): 0  Gene Names: 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
LIJ	F [auth A], G [auth B], I [auth C]	BENZYL [(1S)-2-({(1S,2R)-1-BENZYL-2-HYDROXY-3-[(3-METHOXYBENZYL)AMINO]PROPYL}AMINO)-2-OXO-1-{[(1-PROPYLBUTYL)SULFONYL]METHYL}ETHYL]CARBAMATE C36 H49 N3 O7 S FJYALDRNDKNYKU-LBFZIJHGSA-N
PO4	D [auth A], E [auth A], H [auth C]	PHOSPHATE ION O4 P NBIIXXVUZAFLBC-UHFFFAOYSA-K

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free:  0.253 (Depositor), 0.243 (DCC) 
• R-Value Work:  0.214 (Depositor), 0.206 (DCC) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 82.24	α = 90
b = 104.09	β = 103.46
c = 100.95	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
CNS	refinement
PDB_EXTRACT	data extraction

Structure Validation

Entry History 

Deposition Data

• Released Date: 2007-01-23 
Deposition Author(s): Benson, T.E., Prince, D.B., Tomasselli, A.G., Emmons, T.L., Paddock, D.J.

Revision History  

• Version 1.0: 2007-01-23
  Type: Initial release
  
• Version 1.1: 2008-05-01
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2017-10-18
  Changes: Refinement description
• Version 1.4: 2024-11-06
  Changes: Data collection, Database references, Structure summary