3HVG

Structure of bace (beta secretase) in Complex with EV0

• PDB DOI: https://doi.org/10.2210/pdb3HVG/pdb

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


• Deposited: 2009-06-16 Released: 2009-11-03 
• Deposition Author(s): Godemann, R., Madden, J., Kramer, J., Smith, M.A., Barker, J., Ebneth, A.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.26 Å
• R-Value Free: 0.265 
• R-Value Work: 0.222 
• R-Value Observed: 0.225 

Starting Model: experimental

Literature

Fragment-Based Discovery of BACE1 Inhibitors Using Functional Assays

Godemann, R., Madden, J., Kramer, J., Smith, M.A., Fritz, U., Hesterkamp, T., Barker, J., Hoeppner, S., Hallett, D., Cesura, A., Ebneth, A., Kemp, J.

(2009) Biochemistry 48: 10743-10751

• PubMed: 19799414 
• DOI: https://doi.org/10.1021/bi901061a
• Primary Citation of Related Structures:  
  3HVG, 3HW1


• PubMed Abstract: 
  

  Novel nonpeptidic inhibitors of beta-secretase (BACE1) have been discovered by employing a fragment-based biochemical screening approach. A diverse library of 20000 low-molecular weight compounds were screened and yielded 26 novel hits that were confirmed by biochemical and surface plasmon resonance secondary assays. We describe here fragment inhibitors cocrystallized with BACE1 in a flap open and flap closed conformation as determined by X-ray crystallography.

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Organizational Affiliation: 

Evotec AG, Schnackenburgallee 114, 22525 Hamburg, Germany. [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: 137.93 kDa 
• Atom Count: 9,063 
• Modelled Residue Count: 1,122 
• 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
EV0	D [auth A], E [auth B], F [auth B]	2-amino-6-propylpyrimidin-4(3H)-one C7 H11 N3 O FSYKBAWAYYELHH-UHFFFAOYSA-N
GOL	G [auth C]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
EV0	BindingDB:  3HVG	Kd: 4.45e+6 (nM) from 1 assay(s)
		IC50: 2.49e+6 (nM) from 1 assay(s)
	PDBBind:  3HVG	IC50: 2.00e+6 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.26 Å
• R-Value Free: 0.265 
• R-Value Work: 0.222 
• R-Value Observed: 0.225 
• Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 232.55	α = 90
b = 100.13	β = 103.73
c = 64.78	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2009-11-03 
Deposition Author(s): Godemann, R., Madden, J., Kramer, J., Smith, M.A., Barker, J., Ebneth, A.

Revision History  

• Version 1.0: 2009-11-03
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Non-polymer description, Version format compliance
• Version 1.2: 2018-01-31
  Changes: Experimental preparation
• Version 1.3: 2021-11-10
  Changes: Database references, Derived calculations
• Version 1.4: 2023-11-01
  Changes: Data collection, Refinement description
• Version 1.5: 2024-10-16
  Changes: Structure summary