4B0Q | pdb_00004b0q

Lead Generation of BACE1 Inhibitors by Coupling Non-amidine New Warheads to a Known Binding Scaffold

• PDB DOI: https://doi.org/10.2210/pdb4B0Q/pdb

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


• Deposited: 2012-07-04 Released: 2013-07-24 
• Deposition Author(s): Pendrill, R., Kolmodin, K., Johansson, P., Plobeck, N.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.87 Å
• R-Value Free: 
  0.225 (Depositor), 0.234 (DCC) 
• R-Value Work: 
  0.177 (Depositor), 0.181 (DCC) 
• R-Value Observed: 
  0.180 (Depositor) 

Literature

Lead Generation of Bace1 Inhibitors by Coupling Non-Amidine New Warheads to a Known Binding Scaffold

Pendrill, R., Kolmodin, K., Johansson, P., Plobeck, N.

To be published.

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: 43.32 kDa 
• Atom Count: 3,267 
• Modeled Residue Count: 369 
• Deposited Residue Count: 384 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
BETA-SECRETASE 1	A	384	Homo sapiens	Mutation(s): 0  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
GMF	B [auth A]	2-[[3-(3-methoxyphenyl)phenyl]-(4-pyridyl)methyl]guanidine C20 H20 N4 O LSPQISZRKHVJOD-LJQANCHMSA-N
ACT	C [auth A], D [auth A], E [auth A]	ACETATE ION C2 H3 O2 QTBSBXVTEAMEQO-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.87 Å
• R-Value Free:  0.225 (Depositor), 0.234 (DCC) 
• R-Value Work:  0.177 (Depositor), 0.181 (DCC) 
• R-Value Observed: 0.180 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 47.571	α = 90
b = 76.277	β = 90
c = 103.939	γ = 90

Software Package:

Software Name	Purpose
BUSTER	refinement
MOSFLM	data reduction
SCALA	data scaling
MOLREP	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2013-07-24 
Deposition Author(s): Pendrill, R., Kolmodin, K., Johansson, P., Plobeck, N.

Revision History  

• Version 1.0: 2013-07-24
  Type: Initial release
  
• Version 1.1: 2024-10-23
  Changes: Data collection, Database references, Derived calculations, Other, Structure summary