4I12 | pdb_00004i12

Design and synthesis of thiophene dihydroisoquinolins as novel BACE-1 inhibitors

• PDB DOI: https://doi.org/10.2210/pdb4I12/pdb

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


• Deposited: 2012-11-19 Released: 2013-03-06 
• Deposition Author(s): Lougheed, J.C., Brecht, E., Yao, N.H.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.78 Å
• R-Value Free: 
  0.283 (Depositor), 0.277 (DCC) 
• R-Value Work: 
  0.228 (Depositor), 0.225 (DCC) 
• R-Value Observed: 
  0.231 (Depositor) 

Literature

Design and synthesis of thiophene dihydroisoquinolines as novel BACE1 inhibitors.

Xu, Y.Z., Yuan, S., Bowers, S., Hom, R.K., Chan, W., Sham, H.L., Zhu, Y.L., Beroza, P., Pan, H., Brecht, E., Yao, N., Lougheed, J., Yan, J., Tam, D., Ren, Z., Ruslim, L., Bova, M.P., Artis, D.R.

(2013) Bioorg Med Chem Lett 23: 3075-3080

• PubMed: 23570791 
• DOI: https://doi.org/10.1016/j.bmcl.2013.03.009
• Primary Citation Related Structures: 
  4I0D, 4I0E, 4I0F, 4I12, 4I1C


• PubMed Abstract: 
  

  Utilizing a structure based design approach, combined with extensive medicinal chemistry execution, highly selective, potent and novel BACE1 inhibitor 8 (BACE1 Alpha assay IC50=8nM) was made from a weak μM potency hit in an extremely efficient way. The detailed SAR and general design approaches will be discussed.

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Organizational Affiliation: 
• Department of Chemical Sciences, Elan Pharmaceuticals, 180 Oyster Point Boulevard, South San Francisco, CA 94080, USA. [e-mail]

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly 2  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 2 generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 46.21 kDa 
• Atom Count: 3,157 
• Modeled Residue Count: 374 
• Deposited Residue Count: 406 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Beta-secretase 1	A	406	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 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
1BC	B [auth A]	2-{(1S)-1-{[(1Z)-6-chloro-3,3-dimethyl-3,4-dihydroisoquinolin-1(2H)-ylidene]amino}-2-[2-propyl-4-(1H-pyrazol-4-yl)thiophen-3-yl]ethyl}pyrimidin-4(5H)-one C27 H29 Cl N6 O S SHQGADSMADPNBQ-QFIPXVFZSA-N
ZN	C [auth A], D [auth A], E [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N
NA	F [auth A], G [auth A]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.78 Å
• R-Value Free:  0.283 (Depositor), 0.277 (DCC) 
• R-Value Work:  0.228 (Depositor), 0.225 (DCC) 
• R-Value Observed: 0.231 (Depositor) 

Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 75.458	α = 90
b = 103.122	β = 90
c = 98.835	γ = 90

Software Package:

Software Name	Purpose
CrystalClear	data collection
REFMAC	refinement
CrystalClear	data reduction
CrystalClear	data scaling
REFMAC	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2013-03-06 
Deposition Author(s): Lougheed, J.C., Brecht, E., Yao, N.H.

Revision History  

• Version 1.0: 2013-03-06
  Type: Initial release
  
• Version 1.1: 2013-07-03
  Changes: Database references
• Version 1.2: 2018-01-24
  Changes: Structure summary
• Version 1.3: 2024-11-20
  Changes: Data collection, Database references, Derived calculations, Structure summary