4PZW | pdb_00004pzw

Synthesis, Characterization and PK/PD Studies of a Series of Spirocyclic Pyranochromene BACE1 Inhibitors

• PDB DOI: https://doi.org/10.2210/pdb4PZW/pdb

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


• Deposited: 2014-03-31 Released: 2014-05-14 
• Deposition Author(s): Vigers, G.P.A.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 
  0.231 (Depositor), 0.234 (DCC) 
• R-Value Work: 
  0.202 (Depositor), 0.204 (DCC) 
• R-Value Observed: 
  0.204 (Depositor) 

Literature

Synthesis, characterization, and PK/PD studies of a series of spirocyclic pyranochromene BACE1 inhibitors.

Volgraf, M., Chan, L., Huestis, M.P., Purkey, H.E., Burkard, M., Geck Do, M., Harris, J., Hunt, K.W., Liu, X., Lyssikatos, J.P., Rana, S., Thomas, A.A., Vigers, G.P., Siu, M.

(2014) Bioorg Med Chem Lett 24: 2477-2480

• PubMed: 24780121 
• DOI: https://doi.org/10.1016/j.bmcl.2014.04.012
• Primary Citation Related Structures: 
  4PZW, 4PZX


• PubMed Abstract: 
  

  The development of 1,3,4,4a,5,10a-hexahydropyrano[3,4-b]chromene analogs as BACE1 inhibitors is described. Introduction of the spirocyclic pyranochromene scaffold yielded several advantages over previous generation cores, including increased potency, reduced efflux, and reduced CYP2D6 inhibition. Compound 13 (BACE1 IC50=110 nM) demonstrated a reduction in CSF Aβ in wild type rats after a single dose.

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Organizational Affiliation: 
• Genentech Inc., 1 DNA Way, South San Francisco, CA 94080, United States. Electronic address: [e-mail].
Genentech Inc., 1 DNA Way, South San Francisco, CA 94080, United States.
Array BioPharma, 3200 Walnut Street, Boulder, CO 80301, United States.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 45.88 kDa 
• Atom Count: 3,314 
• Modeled Residue Count: 397 
• 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 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
2X4	C [auth A]	(4R,4a'S,10a'S)-7'-(5-chloropyridin-3-yl)-3',4',4a',10a'-tetrahydro-1'H-spiro[1,3-oxazole-4,5'-pyrano[3,4-b]chromen]-2-amine C19 H18 Cl N3 O3 BGRWOLNAPSRJIS-LSBZLQRGSA-N
NI	B [auth A]	NICKEL (II) ION Ni VEQPNABPJHWNSG-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free:  0.231 (Depositor), 0.234 (DCC) 
• R-Value Work:  0.202 (Depositor), 0.204 (DCC) 
• R-Value Observed: 0.204 (Depositor) 

Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 75.17	α = 90
b = 103.94	β = 90
c = 99.73	γ = 90

Software Package:

Software Name	Purpose
CrystalClear	data collection
MOLREP	phasing
REFMAC	refinement
MOSFLM	data reduction
SCALA	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2014-05-14 
Deposition Author(s): Vigers, G.P.A.

Revision History  

• Version 1.0: 2014-05-14
  Type: Initial release
  
• Version 1.1: 2014-06-18
  Changes: Database references
• Version 1.2: 2014-10-15
  Changes: Structure summary
• Version 1.3: 2024-11-06
  Changes: Data collection, Database references, Derived calculations, Structure summary