3MSJ

Structure of bace (beta secretase) in complex with inhibitor

• PDB DOI: https://doi.org/10.2210/pdb3MSJ/pdb

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


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

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 0.208 
• R-Value Work: 0.177 
• R-Value Observed: 0.177 

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.

---

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)

Biological Assembly 2  

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

Biological assembly 2 assigned by authors and generated by PISA (software)

Biological Assembly 3  

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

Biological assembly 3 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 139.63 kDa 
• Atom Count: 9,702 
• Modelled Residue Count: 1,121 
• Deposited Residue Count: 1,233 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
BETA-SECRETASE 1	A, B, C	411	Homo sapiens	Mutation(s): 2  Gene Names: BACE1 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
EV3	D [auth A], L [auth B], U [auth C]	3-(2-amino-5-chloro-1H-benzimidazol-1-yl)propan-1-ol C10 H12 Cl N3 O NSMVCZCLMLZSOB-UHFFFAOYSA-N
GOL	E [auth A], F [auth A], G [auth A], H [auth A], I [auth A], J [auth A], K [auth A], M [auth B], N [auth B], O [auth B], P [auth B], Q [auth B], R [auth B], S [auth B], T [auth B], V [auth C], W [auth C]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
EV3	PDBBind:  3MSJ	IC50: 7.70e+5 (nM) from 1 assay(s)
	BindingDB:  3MSJ	IC50: 7.70e+5 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 0.208 
• R-Value Work: 0.177 
• R-Value Observed: 0.177 
• Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 229.196	α = 90
b = 98.829	β = 103.36
c = 63.132	γ = 90

Software Package:

Software Name	Purpose
XDS	data scaling
PHASER	phasing
REFMAC	refinement
XDS	data reduction
XSCALE	data scaling

Structure Validation

Entry History 

Deposition Data

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

Revision History  

• Version 1.0: 2010-07-14
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2023-09-06
  Changes: Data collection, Database references, Derived calculations, Refinement description
• Version 1.3: 2024-10-16
  Changes: Structure summary