Biological Assembly 1  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report | Ligand Interaction

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

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 45.83 kDa 
• Atom Count: 3178 
• Modelled Residue Count: 394 
• Deposited Residue Count: 404 
• Unique protein chains: 1

3UDK

Crystal Structure of BACE with Compound 6

• PDB DOI: 10.2210/pdb3UDK/pdb

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


• Deposited: 2011-10-28 Released: 2012-04-18 
• Deposition Author(s): Efremov, I.V., Vajdos, F.F., Borzilleri, K., Capetta, S., Dorff, P., Dutra, J., Mansour, M., Oborski, C., O'Connell, T., O'Sullivan, T.J., Pandit, J., Wang, H., Withka, J.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.51 Å
• R-Value Free: 0.306 
• R-Value Work: 0.219 
• R-Value Observed: 0.223 

Literature

Discovery and optimization of a novel spiropyrrolidine inhibitor of {beta}-secretase (BACE1) through fragment-based drug design.

Efremov, I.V., Vajdos, F.F., Borzilleri, K.A., Capetta, S., Chen, H., Dorff, P.H., Dutra, J.K., Goldstein, S.W., Mansour, M., McColl, A., Noell, S., Oborski, C.E., O'Connell, T.N., O'Sullivan, T.J., Pandit, J., Wang, H., Wei, B., Withka, J.M.

(2012) J Med Chem 55: 9069-9088

• PubMed: 22468999 
• DOI: 10.1021/jm201715d
• Primary Citation of Related Structures:  
  3UDH, 3UDJ, 3UDK, 3UDM, 3UDN, 3UDP, 3UDQ, 3UDR, 3UDY


• PubMed Abstract: 
  

The aspartyl protease β-secretase, or BACE, has been demonstrated to be a key factor in the proteolytic formation of Aβ-peptide, a major component of plaques in the brains of Alzheimer's disease (AD) patients, and inhibition of this enzyme has emerged as a major strategy for pharmacologic intervention in AD. An X-ray-based fragment screen of Pfizer's proprietary fragment collection has resulted in the identification of a novel BACE binder featuring spiropyrrolidine framework. Although exhibiting only weak inhibitory activity against the BACE enzyme, the small compound was verified by biophysical and NMR-based methods as a bona fide BACE inhibitor. Subsequent optimization of the lead compound, relying heavily on structure-based drug design and computational prediction of physiochemical properties, resulted in a nearly 1000-fold improvement in potency while maintaining ligand efficiency and properties predictive of good permeability and low P-gp liability.

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Related Citations: 

• High yield expression of human BACE constructs in Escherichia coli for refolding, purification, and high resolution diffracting crystal forms.
  Tomasselli, A.G., Paddock, D.J., Emmons, T.L., Mildner, A.M., Leone, J.W., Lull, J.M., Cialdella, J.I., Prince, D.B., Fischer, H.D., Heinrikson, R.L., Benson, T.E.
  (2008) Protein Pept Lett 15: 131

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Organizational Affiliation: 

Pfizer Worldwide Research, Groton Laboratories, Eastern Point Road, Groton, Connecticut 06340, United States. [e-mail]

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Beta-secretase 1	A	404	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 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
095	B [auth A]	tetrahydro-2H-pyran-4-yl (3S,5'R)-2-oxo-1,2-dihydrospiro[indole-3,3'-pyrrolidine]-5'-carboxylate C17 H20 N2 O4 HIOAPSYSJQPIRC-RHSMWYFYSA-N
PEG	E [auth A]	DI(HYDROXYETHYL)ETHER C4 H10 O3 MTHSVFCYNBDYFN-UHFFFAOYSA-N
ZN	F [auth A], G [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N
EDO	C [auth A], D [auth A]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
095	BindingDB:  3UDK	IC50: min: 3.20e+4, max: 1.14e+5 (nM) from 2 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.51 Å
• R-Value Free: 0.306 
• R-Value Work: 0.219 
• R-Value Observed: 0.223 
• Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 74.797	α = 90
b = 104.425	β = 90
c = 101.333	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2011-10-28 
• Released Date: 2012-04-18 
Deposition Author(s): Efremov, I.V., Vajdos, F.F., Borzilleri, K., Capetta, S., Dorff, P., Dutra, J., Mansour, M., Oborski, C., O'Connell, T., O'Sullivan, T.J., Pandit, J., Wang, H., Withka, J.

Revision History  

• Version 1.0: 2012-04-18
  Type: Initial release
  
• Version 1.1: 2013-06-19
  Changes: Database references
• Version 1.2: 2017-11-08
  Changes: Refinement description
• Version 1.3: 2018-04-04
  Changes: Data collection