2IRZ | pdb_00002irz

Crystal structure of human Beta-secretase complexed with inhibitor

• PDB DOI: https://doi.org/10.2210/pdb2IRZ/pdb

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


• Deposited: 2006-10-16 Released: 2006-11-14 
• Deposition Author(s): Munshi, S.

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 
  0.240 (Depositor) 
• R-Value Work: 
  0.219 (Depositor) 
• R-Value Observed: 
  0.219 (Depositor) 

Starting Model: experimental

Literature

Discovery of oxadiazoyl tertiary carbinamine inhibitors of beta-secretase (BACE-1).

Rajapakse, H.A., Nantermet, P.G., Selnick, H.G., Munshi, S., McGaughey, G.B., Lindsley, S.R., Young, M.B., Lai, M.T., Espeseth, A.S., Shi, X.P., Colussi, D., Pietrak, B., Crouthamel, M.C., Tugusheva, K., Huang, Q., Xu, M., Simon, A.J., Kuo, L., Hazuda, D.J., Graham, S., Vacca, J.P.

(2006) J Med Chem 49: 7270-7273

• PubMed: 17149856 
• DOI: https://doi.org/10.1021/jm061046r
• Primary Citation of Related Structures:  
  2IRZ, 2IS0


• PubMed Abstract: 
  

  We describe the discovery and optimization of tertiary carbinamine derived inhibitors of the enzyme beta-secretase (BACE-1). These novel non-transition-state-derived ligands incorporate a single primary amine to interact with the catalytic aspartates of the target enzyme. Optimization of this series provided inhibitors with intrinsic and functional potency comparable to evolved transition state isostere derived inhibitors of BACE-1.

---

Organizational Affiliation: 

Department of Medicinal Chemistry, Merck Research Laboratories, P.O. Box 4, West Point, Pennsylvania 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: 45.67 kDa 
• Atom Count: 3,312 
• 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) Explore P56817  Go to UniProtKB:  P56817
PHAROS:  P56817 GTEx:  ENSG00000186318

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
I02	B [auth A]	3-{5-[(1R)-1-AMINO-1-METHYL-2-PHENYLETHYL]-1,3,4-OXADIAZOL-2-YL}-N-[(1R)-1-(4-FLUOROPHENYL)ETHYL]-5-[METHYL(METHYLSULFONYL)AMINO]BENZAMIDE C28 H30 F N5 O4 S QEJSJQVKMSAHHX-KWMCUTETSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
I02	BindingDB:  2IRZ	IC50: min: 9, max: 60 (nM) from 3 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free:  0.240 (Depositor) 
• R-Value Work:  0.219 (Depositor) 
• R-Value Observed: 0.219 (Depositor) 

Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 104.53	α = 90
b = 127.78	β = 90
c = 76.47	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2006-11-14 
Deposition Author(s): Munshi, S.

Revision History  

• Version 1.0: 2006-11-14
  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: 2023-08-30
  Changes: Data collection, Refinement description
• Version 1.5: 2024-10-16
  Changes: Structure summary