5DQC | pdb_00005dqc

Co-crystal of BACE1 with compound 0211

• PDB DOI: https://doi.org/10.2210/pdb5DQC/pdb

• Classification: Hydrolase/Hydrolase Inhibitor
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2015-09-14 Released: 2016-02-17 
• Deposition Author(s): Ghosh, A.K., Bhavanam, S.R., Yen, T.-C., Cardenas, E.L., Rao, K.V., Downs, D., Huang, X., Tang, J., Mescar, A.D.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.47 Å
• R-Value Free: 
  0.235 (Depositor), 0.241 (DCC) 
• R-Value Work: 
  0.185 (Depositor), 0.195 (DCC) 
• R-Value Observed: 
  0.187 (Depositor) 

Literature

Design of Potent and Highly Selective Inhibitors for Human beta-Secretase 2 (Memapsin 1), a Target for Type 2 Diabetes.

Ghosh, A.K., Reddy, B.S., Yen, Y.C., Cardenas, E., Rao, K.V., Downs, D., Huang, X., Tang, J., Mesecar, A.D.

(2016) Chem Sci 7: 3117-3122

• PubMed: 27347366 
• DOI: https://doi.org/10.1039/C5SC03718B
• Primary Citation Related Structures: 
  5DQC


• PubMed Abstract: 
  

  Design, synthesis and evaluation of very potent and selective β-Secretase 2 (memapsin 1, BACE 2) inhibitors are described. The inhibitors were designed specifically to interact with the S2'-site of β-secretase 2 to provide >170,000-fold selectivity over β-secretase (BACE 1) and >15,000-fold selectivity over cathepsin D. BACE 2 is implicated in Type 2 diabetes. The studies serve as an important guide to selective BACE 2 inhibitors.

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Organizational Affiliation: 
• Department of Chemistry and Department of Medicinal Chemistry, Purdue University, West Lafayette, IN 47907 (USA).
Department of Biological Sciences, Purdue University, West Lafayette, IN 47907 (USA).
Protein Studies Program, Oklahoma Medical Research Foundation, University of Oklahoma, Oklahoma City, OK 73104 (USA).
Department of Biological Sciences, Purdue University, West Lafayette, IN 47907 (USA); Department of Chemistry and Department of Medicinal Chemistry, Purdue University, West Lafayette, IN 47907 (USA); Department of Biochemistry, Purdue University, West Lafayette, IN 47907 (USA).

Biological Assembly 1  

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

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly 2  

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

Biological assembly 2 assigned by authors and generated by PISA (software)

Biological Assembly 3  

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

Biological assembly 3 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 132.37 kDa 
• Atom Count: 9,054 
• Modeled Residue Count: 1,114 
• Deposited Residue Count: 1,170 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Beta-secretase 1	A, B, C	390	Homo sapiens	Mutation(s): 0  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 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
5E7	D [auth A], E [auth B], F [auth C]	N-[(2S,3R)-3-hydroxy-4-({(2S,3S)-3-hydroxy-1-[(2-methylpropyl)amino]-1-oxobutan-2-yl}amino)-1-phenylbutan-2-yl]-5-[methyl(methylsulfonyl)amino]-N'-[(1R)-1-phenylethyl]benzene-1,3-dicarboxamide C36 H49 N5 O7 S ZIEVAMMZKBNDFB-AAZBAGLXSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.47 Å
• R-Value Free:  0.235 (Depositor), 0.241 (DCC) 
• R-Value Work:  0.185 (Depositor), 0.195 (DCC) 
• R-Value Observed: 0.187 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 81.95	α = 90
b = 103.403	β = 102.66
c = 100.834	γ = 90

Software Package:

Software Name	Purpose
HKL-2000	data reduction
HKL-2000	data scaling
PHENIX	refinement
PDB_EXTRACT	data extraction

Structure Validation

Entry History 

Deposition Data

• Released Date: 2016-02-17 
Deposition Author(s): Ghosh, A.K., Bhavanam, S.R., Yen, T.-C., Cardenas, E.L., Rao, K.V., Downs, D., Huang, X., Tang, J., Mescar, A.D.

Revision History  

• Version 1.0: 2016-02-17
  Type: Initial release
  
• Version 1.1: 2016-07-13
  Changes: Database references
• Version 1.2: 2024-11-20
  Changes: Data collection, Database references, Derived calculations, Structure summary