2Q15

Structure of BACE complexed to compound 3a

• PDB DOI: https://doi.org/10.2210/pdb2Q15/pdb

• Classification: HYDROLASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2007-05-23 Released: 2007-08-14 
• Deposition Author(s): Sharff, A.J.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Free: 0.344 
• R-Value Work: 0.252 
• R-Value Observed: 0.256 

Literature

2-Amino-3,4-dihydroquinazolines as inhibitors of BACE-1 (beta-Site APP cleaving enzyme): Use of structure based design to convert a micromolar hit into a nanomolar lead.

Baxter, E.W., Conway, K.A., Kennis, L., Bischoff, F., Mercken, M.H., Winter, H.L., Reynolds, C.H., Tounge, B.A., Luo, C., Scott, M.K., Huang, Y., Braeken, M., Pieters, S.M., Berthelot, D.J., Masure, S., Bruinzeel, W.D., Jordan, A.D., Parker, M.H., Boyd, R.E., Qu, J., Alexander, R.S., Brenneman, D.E., Reitz, A.B.

(2007) J Med Chem 50: 4261-4264

• PubMed: 17685503 
• DOI: https://doi.org/10.1021/jm0705408
• Primary Citation of Related Structures:  
  2Q11, 2Q15


• PubMed Abstract: 
  

  A new aspartic protease inhibitory chemotype bearing a 2-amino-3,4-dihydroquinazoline ring was identified by high-throughput screening for the inhibition of BACE-1. X-ray crystallography revealed that the exocyclic amino group participated in a hydrogen bonding array with the two catalytic aspartic acids of BACE-1 (Asp(32), Asp(228)). BACE-1 inhibitory potency was increased (0.9 microM to 11 nM K(i)) by substitution into the unoccupied S(1)' pocket.

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Organizational Affiliation: 

Johnson & Johnson Pharmaceutical Research and Development, LLC, Spring House, Pennsylvania 19477, USA. [e-mail]

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 43.48 kDa 
• Atom Count: 3,217 
• Modelled Residue Count: 385 
• Deposited Residue Count: 385 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Beta-secretase 1	A	385	Homo sapiens	Mutation(s): 4  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 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
3MR	B [auth A]	(4S)-4-(2-AMINO-6-PHENOXYQUINAZOLIN-3(4H)-YL)-N,4-DICYCLOHEXYL-N-METHYLBUTANAMIDE C31 H42 N4 O2 JKQCQYBXDQPJNC-LJAQVGFWSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
3MR	PDBBind:  2Q15	Ki: 11 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Free: 0.344 
• R-Value Work: 0.252 
• R-Value Observed: 0.256 
• Space Group: P 6₁ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 102.347	α = 90
b = 102.347	β = 90
c = 169.715	γ = 120

Software Package:

Software Name	Purpose
REFMAC	refinement

Structure Validation

Entry History 

Deposition Data

• Released Date: 2007-08-14 
Deposition Author(s): Sharff, A.J.

Revision History  

• Version 1.0: 2007-08-14
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2021-10-20
  Changes: Database references, Derived calculations
• Version 1.3: 2024-10-16
  Changes: Data collection, Structure summary