3S2O | pdb_00003s2o

Fragment based discovery and optimisation of bace-1 inhibitors

• PDB DOI: https://doi.org/10.2210/pdb3S2O/pdb
• Entry: 3S2O supersedes: 3MSM

• Classification: HYDROLASE/HYDROLASE INHIBITOR
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2011-05-17 Released: 2011-06-01 
• Deposition Author(s): Madden, J., Godemann, R., Smith, M.A., Hallett, D., Barker, J., Kraemer, J.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.60 Å
• R-Value Free: 
  0.261 (Depositor), 0.270 (DCC) 
• R-Value Work: 
  0.205 (Depositor), 0.210 (DCC) 
• R-Value Observed: 
  0.208 (Depositor) 

Starting Model: experimental

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]

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: 46.09 kDa 
• Atom Count: 3,073 
• Modelled Residue Count: 378 
• Deposited Residue Count: 408 
• Unique protein chains: 1

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 GTEx:  ENSG00000186318

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
EV6	B [auth A]	(3S)-3-(2-amino-5-chloro-1H-benzimidazol-1-yl)-N-[(1R,3S,5R,7R)-tricyclo[3.3.1.1~3,7~]dec-2-yl]pentanamide C22 H29 Cl N4 O KMAKOMVKNWTGPE-LIXZBVSLSA-N
IOD	C [auth A], D [auth A]	IODIDE ION I XMBWDFGMSWQBCA-UHFFFAOYSA-M

Binding Affinity Annotations
ID	Source	Binding Affinity
EV6	BindingDB:  3S2O	IC50: 8900 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.60 Å
• R-Value Free:  0.261 (Depositor), 0.270 (DCC) 
• R-Value Work:  0.205 (Depositor), 0.210 (DCC) 
• R-Value Observed: 0.208 (Depositor) 

Space Group: P 6₁ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 101.88	α = 90
b = 101.88	β = 90
c = 170.181	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: 2011-06-01 
Deposition Author(s): Madden, J., Godemann, R., Smith, M.A., Hallett, D., Barker, J., Kraemer, J.
• This entry supersedes: 3MSM

Revision History  

• Version 1.0: 2011-06-01
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2011-09-07
  Changes: Structure summary
• Version 1.3: 2023-09-13
  Changes: Data collection, Database references, Derived calculations, Refinement description
• Version 1.4: 2024-11-27
  Changes: Structure summary