Biological Assembly 1  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report | Ligand Interaction

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

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

Macromolecule Content

• Total Structure Weight: 43.62 kDa 
• Atom Count: 3267 
• Modelled Residue Count: 376 
• Deposited Residue Count: 388 
• Unique protein chains: 1

4B77

Aminoimidazoles as BACE-1 Inhibitors: From De Novo Design to Ab- lowering in Brain

• PDB DOI: 10.2210/pdb4B77/pdb

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


• Deposited: 2012-08-16 Released: 2013-06-26 
• Deposition Author(s): Gravenfors, Y., Blid, J., Ginman, T., Karlstrom, S., Kihlstrom, J., Kolmodin, K., Lindstrom, J., Berg, S., Kieseritzky, F., Slivo, C., Swahn, B., Viklund, J., Olsson, L., Johansson, P., Eketjall, S., Falting, J., Jeppsson, F., Stromberg, K., Janson, J., Rahm, F.

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 0.248 
• R-Value Work: 0.195 
• R-Value Observed: 0.198 

Literature

Core Refinement Toward Permeable Beta-Secretase (Bace-1) Inhibitors with Low Herg Activity.

Ginman, T., Viklund, J., Malmstrom, J., Blid, J., Emond, R., Forsblom, R., Johansson, A., Kers, A., Lake, F., Sehgelmeble, F., Sterky, K.J., Bergh, M., Lindgren, A., Johansson, P., Jeppsson, F., Falting, J., Gravenfors, Y., Rahm, F.

(2013) J Med Chem 56: 4181

• PubMed: 23126626 
• DOI: 10.1021/jm3011349
• Primary Citation of Related Structures:  
  4B70, 4B72, 4B77, 4B78


• PubMed Abstract: 
  

By use of iterative design aided by predictive models for target affinity, brain permeability, and hERG activity, novel and diverse compounds based on cyclic amidine and guanidine cores were synthesized with the goal of finding BACE-1 inhibitors as a treatment for Alzheimer's disease. Since synthesis feasibility had low priority in the design of the cores, an extensive synthesis effort was needed to make the relevant compounds. Syntheses of these compounds are reported, together with physicochemical properties and structure-activity relationships based on in vitro data. Four crystal structures of diverse amidines binding in the active site are deposited and discussed. Inhibitors of BACE-1 with 3 μM to 32 nM potencies in cells are shown, together with data on in vivo brain exposure levels for four compounds. The results presented show the importance of the core structure for the profile of the final compounds.

---

Organizational Affiliation: 

Department of Medicinal Chemistry, AstraZeneca R&D Södertälje, SE-151 85, Södertälje, Sweden.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
BETA-SECRETASE 1	A	388	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
54M	C [auth A]	(5R)-5-(4-methoxyphenyl)-5-(3-pyrimidin-5-ylphenyl)-3,4-dihydropyrrol-2-amine C21 H20 N4 O MLDNPVIFXVSEGX-OAQYLSRUSA-N
DMS	B [auth A]	DIMETHYL SULFOXIDE C2 H6 O S IAZDPXIOMUYVGZ-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
54M	PDBBind:  4B77	IC50: 7900 (nM) from 1 assay(s)
	Binding MOAD:  4B77	IC50: 7900 (nM) from 1 assay(s)
	BindingDB:  4B77	IC50: min: 2000, max: 7900 (nM) from 2 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 0.248 
• R-Value Work: 0.195 
• R-Value Observed: 0.198 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 47.885	α = 90
b = 75.636	β = 90
c = 104.613	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
MOSFLM	data reduction
SCALA	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2012-08-16 
• Released Date: 2013-06-26 
Deposition Author(s): Gravenfors, Y., Blid, J., Ginman, T., Karlstrom, S., Kihlstrom, J., Kolmodin, K., Lindstrom, J., Berg, S., Kieseritzky, F., Slivo, C., Swahn, B., Viklund, J., Olsson, L., Johansson, P., Eketjall, S., Falting, J., Jeppsson, F., Stromberg, K., Janson, J., Rahm, F.

Revision History  

• Version 1.0: 2013-06-26
  Type: Initial release
  
• Version 1.1: 2013-07-03
  Changes: Database references