4H3G

Structure of BACE Bound to 2-((7aR)-7a-(4-(3-cyanophenyl)thiophen-2-yl)-2-imino-3-methyl-4-oxohexahydro-1H-pyrrolo[3,4-d]pyrimidin-6(2H)-yl)nicotinonitrile

• PDB DOI:  https://doi.org/10.2210/pdb4H3G/pdb

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


• Deposited: 2012-09-13 Released: 2012-11-07 
• Deposition Author(s): Strickland, C., Mandal, M.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.85 Å
• R-Value Free: 0.228 
• R-Value Work: 0.193 

Literature

Design and Validation of Bicyclic Iminopyrimidinones As Beta Amyloid Cleaving Enzyme-1 (BACE1) Inhibitors: Conformational Constraint to Favor a Bioactive Conformation.

Mandal, M., Zhu, Z., Cumming, J.N., Liu, X., Strickland, C., Mazzola, R.D., Caldwell, J.P., Leach, P., Grzelak, M., Hyde, L., Zhang, Q., Terracina, G., Zhang, L., Chen, X., Kuvelkar, R., Kennedy, M.E., Favreau, L., Cox, K., Orth, P., Buevich, A., Voigt, J., Wang, H., Kazakevich, I., McKittrick, B.A., Greenlee, W., Parker, E.M., Stamford, A.W.

(2012) J Med Chem 55: 9331-9345

• PubMed: 22989333 
• DOI: https://doi.org/10.1021/jm301039c
• Primary Citation of Related Structures:  
  4H1E, 4H3F, 4H3G, 4H3I, 4H3J, 4HA5


• PubMed Abstract: 
  

On the basis of our observation that the biaryl substituent of iminopyrimidinone 7 must be in a pseudoaxial conformation to occupy the contiguous S1-S3 subsites of BACE1, we have designed a novel fused bicyclic iminopyrimidinone scaffold intended to favor this bioactive conformation. Strategic incorporation of a nitrogen atom in the new constrained ring allowed us to develop SAR around the S2' binding pocket and ultimately resulted in analogues with low nanomolar potency for BACE1. In particular, optimization of the prime side substituent led to major improvements in potency by displacement of two conserved water molecules from a region near S2'. Further optimization of the pharmacokinetic properties of this fused pyrrolidine series, in conjunction with facile access to a rat pharmacodynamic model, led to identification of compound 43, which is an orally active, brain penetrant inhibitor that reduces Aβ(40) in the plasma, CSF, and cortex of rats in a dose-dependent manner.

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Organizational Affiliation: 

Department of Medicinal Chemistry, Merck Research Laboratories, 2015 Galloping Hill Road, Kenilworth, New Jersey 07033, United States. [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: 93.86 kDa 
• Atom Count: 7,070 
• Modelled Residue Count: 779 
• Deposited Residue Count: 828 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Beta-secretase 1	A, B	414	Homo sapiens	Mutation(s): 0  Gene Names: BACE, BACE1, 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

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
10Q	D [auth A], G [auth B]	2-{(2E,4aR,7aR)-7a-[4-(3-cyanophenyl)thiophen-2-yl]-2-imino-3-methyl-4-oxooctahydro-6H-pyrrolo[3,4-d]pyrimidin-6-yl}pyridine-3-carbonitrile C24 H19 N7 O S LWVMTILRDSZVMA-CYFREDJKSA-N
TLA	C [auth A], E [auth B], F [auth B]	L(+)-TARTARIC ACID C4 H6 O6 FEWJPZIEWOKRBE-JCYAYHJZSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
10Q	PDBBind:  4H3G	Ki: 6 (nM) from 1 assay(s)
	Binding MOAD:  4H3G	Ki: 6 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.85 Å
• R-Value Free: 0.228 
• R-Value Work: 0.193 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 86.39	α = 90
b = 90.03	β = 90
c = 131.555	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2012-11-07 
Deposition Author(s): Strickland, C., Mandal, M.

Revision History  

• Version 1.0: 2012-11-07
  Type: Initial release
  
• Version 1.1: 2012-11-21
  Changes: Database references