2VA5

X-ray crystal structure of beta secretase complexed with compound 8c

• PDB DOI:  https://doi.org/10.2210/pdb2VA5/pdb

• Classification: HYDROLASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): Yes 


• Deposited: 2007-08-30 Released: 2007-11-13 
• Deposition Author(s): Edwards, P.D., Albert, J.S., Sylvester, M., Aharony, D., Andisik, D., Callaghan, O., Campbell, J.B., Carr, R.A., Chessari, G., Congreve, M., Frederickson, M., Folmer, R.H.A., Geschwindner, S., Koether, G., Kolmodin, K., Krumrine, J., Mauger, R.C., Murray, C.W., Olsson, L., Patel, S., Spear, N., Tian, G.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.75 Å
• R-Value Free: 0.319 
• R-Value Work: 0.228 
• R-Value Observed: 0.232 

Literature

Application of Fragment-Based Lead Generation to the Discovery of Novel, Cyclic Amidine Beta-Secretase Inhibitors with Nanomolar Potency, Cellular Activity, and High Ligand Efficiency.

Edwards, P.D., Albert, J.S., Sylvester, M., Aharony, D., Andisik, D., Callaghan, O., Campbell, J.B., Carr, R.A., Chessari, G., Congreve, M., Frederickson, M., Folmer, R.H., Geschwindner, S., Koether, G., Kolmodin, K., Krumrine, J., Mauger, R.C., Murray, C.W., Olsson, L.L., Patel, S., Spear, N., Tian, G.

(2007) J Med Chem 50: 5912

• PubMed: 17985862 
• DOI: https://doi.org/10.1021/jm070829p
• Primary Citation of Related Structures:  
  2VA5, 2VA6, 2VA7


• PubMed Abstract: 
  

Fragment-based lead generation has led to the discovery of a novel series of cyclic amidine-based inhibitors of beta-secretase (BACE-1). Initial fragment hits with an isocytosine core having millimolar potency were identified via NMR affinity screening. Structure-guided evolution of these fragments using X-ray crystallography together with potency determination using surface plasmon resonance and functional enzyme inhibition assays afforded micromolar inhibitors. Similarity searching around the isocytosine core led to the identification of a related series of inhibitors, the dihydroisocytosines. By leveraging the knowledge of the ligand-BACE-1 recognition features generated from the isocytosines, the dihydroisocytosines were efficiently optimized to submicromolar potency. Compound 29, with an IC50 of 80 nM, a ligand efficiency of 0.37, and cellular activity of 470 nM, emerged as the lead structure for future optimization.

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Organizational Affiliation: 

CNS Discovery Research, AstraZeneca Pharmaceuticals LP, 1800 Concord Pike, Wilmington, DE 19850-5437, USA. [e-mail]

Biological Assembly 1  

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

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

Macromolecule Content

• Total Structure Weight: 50.7 kDa 
• Atom Count: 3,055 
• Modelled Residue Count: 378 
• Deposited Residue Count: 455 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
BETA-SECRETASE 1 .	A	455	Homo sapiens	Mutation(s): 2  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

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
C8C	D [auth A]	2-amino-6-[2-(1H-indol-6-yl)ethyl]pyrimidin-4(3H)-one C14 H14 N4 O VRAZIAJSKFRSIP-UHFFFAOYSA-N
IOD	B [auth A], C [auth A]	IODIDE ION I XMBWDFGMSWQBCA-UHFFFAOYSA-M

Binding Affinity Annotations
ID	Source	Binding Affinity
C8C	PDBBind:  2VA5	IC50: 8.60e+4 (nM) from 1 assay(s)
	BindingDB:  2VA5	IC50: min: 8.60e+4, max: 1.30e+5 (nM) from 2 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.75 Å
• R-Value Free: 0.319 
• R-Value Work: 0.228 
• R-Value Observed: 0.232 
• Space Group: P 6₁ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 102.138	α = 90
b = 102.138	β = 90
c = 168.258	γ = 120

Software Package:

Software Name	Purpose
REFMAC	refinement
MOSFLM	data reduction
SCALA	data scaling
C-SEARCH	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2007-11-13 
Deposition Author(s): Edwards, P.D., Albert, J.S., Sylvester, M., Aharony, D., Andisik, D., Callaghan, O., Campbell, J.B., Carr, R.A., Chessari, G., Congreve, M., Frederickson, M., Folmer, R.H.A., Geschwindner, S., Koether, G., Kolmodin, K., Krumrine, J., Mauger, R.C., Murray, C.W., Olsson, L., Patel, S., Spear, N., Tian, G.

Revision History  

• Version 1.0: 2007-11-13
  Type: Initial release
  
• Version 1.1: 2011-05-08
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance