3CID

Structure of BACE Bound to SCH726222

• PDB DOI: https://doi.org/10.2210/pdb3CID/pdb

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


• Deposited: 2008-03-11 Released: 2008-06-10 
• Deposition Author(s): Strickland, C., Cumming, J.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 0.221 
• R-Value Work: 0.194 

Literature

Rational design of novel, potent piperazinone and imidazolidinone BACE1 inhibitors

Cumming, J.N., Le, T.X., Babu, S., Carroll, C., Chen, X., Favreau, L., Gaspari, P., Guo, T., Hobbs, D.W., Huang, Y., Iserloh, U., Kennedy, M.E., Kuvelkar, R., Li, G., Lowrie, J., McHugh, N.A., Ozgur, L., Pan, J., Parker, E.M., Saionz, K., Stamford, A.W., Strickland, C., Tadesse, D., Voigt, J., Wang, L., Wu, Y., Zhang, L., Zhang, Q.

(2008) Bioorg Med Chem Lett 18: 3236-3241

• PubMed: 18468890 
• DOI: https://doi.org/10.1016/j.bmcl.2008.04.050
• Primary Citation of Related Structures:  
  3CIB, 3CIC, 3CID


• PubMed Abstract: 
  

  Guided by structure-based design, we synthesized two novel series of potent inhibitors of BACE1 and generated extensive SAR around both the prime and non-prime side binding pockets. The key feature of both series is a cyclic amine motif specifically crafted to achieve interactions with both the flap and with the S2' pocket.

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Organizational Affiliation: 

Schering-Plough Research Institute, 2015 Galloping Hill Road, Kenilworth, NJ 07033, USA. [e-mail]

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)

Macromolecule Content

• Total Structure Weight: 88.52 kDa 
• Atom Count: 7,183 
• Modelled Residue Count: 779 
• Deposited Residue Count: 780 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Beta-secretase 1	A, B	390	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 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
318	C [auth A], E [auth B]	N'-[(1S,2S)-2-[(4S)-1-benzyl-5-oxoimidazolidin-4-yl]-1-(3,5-difluorobenzyl)-2-hydroxyethyl]-5-methyl-N,N-dipropylbenzene-1,3-dicarboxamide C34 H40 F2 N4 O4 HZWNNIVRFLRAQW-CHQNGUEUSA-N
TAR	D [auth A], F [auth B], G [auth B]	D(-)-TARTARIC ACID C4 H6 O6 FEWJPZIEWOKRBE-LWMBPPNESA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
318	PDBBind:  3CID	IC50: 5 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 0.221 
• R-Value Work: 0.194 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 86.296	α = 90
b = 89.131	β = 90
c = 130.59	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2008-06-10 
Deposition Author(s): Strickland, C., Cumming, J.

Revision History  

• Version 1.0: 2008-06-10
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2017-10-25
  Changes: Refinement description
• Version 1.3: 2024-10-30
  Changes: Data collection, Database references, Derived calculations, Structure summary