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: 46 kDa 
• Atom Count: 3,275 
• Modelled Residue Count: 378 
• Deposited Residue Count: 408 
• Unique protein chains: 1

 3MSK

Fragment Based Discovery and Optimisation of BACE-1 Inhibitors

• PDB DOI:  https://doi.org/10.2210/pdb3MSK/pdb

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


• Deposited: 2010-04-29 Released: 2010-07-14 
• Deposition Author(s): Smith, M.A., Madden, J.M., Barker, J., Godemann, R., Kraemer, J., Hallett, D.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 0.264 
• R-Value Work: 0.223 
• R-Value Observed: 0.225 

Literature

Fragment-based discovery and optimization of BACE1 inhibitors.

Madden, J., Dod, J.R., Godemann, R., Kraemer, J., Smith, M., Biniszkiewicz, M., Hallett, D.J., Barker, J., Dyekjaer, J.D., Hesterkamp, T.

(2010) Bioorg Med Chem Lett 20: 5329-5333

• PubMed: 20656487 
• DOI: https://doi.org/10.1016/j.bmcl.2010.06.089
• Primary Citation of Related Structures:  
  3MSJ, 3MSK, 3MSL, 3S2O


• PubMed Abstract: 
  

A novel series of 2-aminobenzimidazole inhibitors of BACE1 has been discovered using fragment-based drug discovery (FBDD) techniques. The rapid optimization of these inhibitors using structure-guided medicinal chemistry is discussed.

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Organizational Affiliation: 

Evotec UK Ltd, Abingdon, UK. [e-mail]

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Beta-secretase 1	A	408	Homo sapiens	Mutation(s): 0  Gene Names: BACE, BACE1, 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 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
EV4	D [auth A]	4-(2-amino-5-chloro-1H-benzimidazol-1-yl)-N-cyclohexyl-N-methylbutanamide C18 H25 Cl N4 O UIWHCBCBZBYNDS-UHFFFAOYSA-N
IOD	B [auth A]	IODIDE ION I XMBWDFGMSWQBCA-UHFFFAOYSA-M
GOL	C [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
EV4	PDBBind:  3MSK	IC50: 2.60e+4 (nM) from 1 assay(s)
	Binding MOAD:  3MSK	IC50: 2.60e+4 (nM) from 1 assay(s)
	BindingDB:  3MSK	IC50: 2.60e+4 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 0.264 
• R-Value Work: 0.223 
• R-Value Observed: 0.225 
• Space Group: P 6₁ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 102.51	α = 90
b = 102.51	β = 90
c = 170.528	γ = 120

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2010-07-14 
Deposition Author(s): Smith, M.A., Madden, J.M., Barker, J., Godemann, R., Kraemer, J., Hallett, D.

Revision History  

• Version 1.0: 2010-07-14
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2018-01-24
  Changes: Advisory, Structure summary