3K5C

Human BACE-1 complex with NB-216

• PDB DOI:  https://doi.org/10.2210/pdb3K5C/pdb

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


• Deposited: 2009-10-07 Released: 2010-03-02 
• Deposition Author(s): Rondeau, J.-M.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.12 Å
• R-Value Free: 0.220 
• R-Value Work: 0.200 
• R-Value Observed: 0.202 

Literature

Macrocyclic BACE-1 inhibitors acutely reduce Abeta in brain after po application.

Lerchner, A., Machauer, R., Betschart, C., Veenstra, S., Rueeger, H., McCarthy, C., Tintelnot-Blomley, M., Jaton, A.L., Rabe, S., Desrayaud, S., Enz, A., Staufenbiel, M., Paganetti, P., Rondeau, J.M., Neumann, U.

(2010) Bioorg Med Chem Lett 20: 603-607

• PubMed: 19963375 
• DOI: https://doi.org/10.1016/j.bmcl.2009.11.092
• Primary Citation of Related Structures:  
  3K5C


• PubMed Abstract: 
  

A series of macrocyclic peptidic BACE-1 inhibitors was designed. While potency on BACE-1 was rather high, the first set of compounds showed poor brain permeation and high efflux in the MDRI-MDCK assay. The replacement of the secondary benzylamino group with a phenylcyclopropylamino group maintained potency on BACE-1, while P-glycoprotein-mediated efflux was significantly reduced and brain permeation improved. Several compounds from this series demonstrated acute reduction of Abeta in human APP-wildtype transgenic (APP51/16) mice after oral administration.

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Related Citations: 

• Macrocyclic peptidomimetic beta-secretase (BACE-1) inhibitors with activity in vivo
  Machauer, R., Laumen, K., Veenstra, S., Rondeau, J.-M., Tintelnot-Blomley, M., Betschart, C., Jaton, A.-L., Desrayaud, S., Staufenbiel, M., Rabe, S., Paganetti, P., Neumann, U.
  (2009) Bioorg Med Chem Lett 19: 1366

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Organizational Affiliation: 

Novartis Institutes for BioMedicalResearch, Novartis Pharma AG, PO Box, CH 4002, Basel, Switzerland. [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: 136.05 kDa 
• Atom Count: 9,519 
• Modelled Residue Count: 1,135 
• Deposited Residue Count: 1,206 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Beta-secretase 1	A, B, C	402	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 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
0BI	D [auth A], E [auth B], F [auth C]	(4S)-4-[(1R)-1-hydroxy-2-({1-[3-(1-methylethyl)phenyl]cyclopropyl}amino)ethyl]-19-(methoxymethyl)-11-oxa-3,16-diazatric yclo[15.3.1.1~6,10~]docosa-1(21),6(22),7,9,17,19-hexaen-2-one C35 H45 N3 O4 GCZHKZTYTMTFGU-JHOUSYSJSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
0BI	BindingDB:  3K5C	IC50: min: 17, max: 20 (nM) from 2 assay(s)
	PDBBind:  3K5C	IC50: 17 (nM) from 1 assay(s)
	Binding MOAD:  3K5C	IC50: 17 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.12 Å
• R-Value Free: 0.220 
• R-Value Work: 0.200 
• R-Value Observed: 0.202 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 81.752	α = 90
b = 103.186	β = 104.44
c = 100.144	γ = 90

Software Package:

Software Name	Purpose
XSCALE	data scaling
CNS	refinement
PDB_EXTRACT	data extraction
XDS	data reduction
CNX	phasing
CNX	refinement

Structure Validation

Entry History 

Deposition Data

• Released Date: 2010-03-02 
Deposition Author(s): Rondeau, J.-M.

Revision History  

• Version 1.0: 2010-03-02
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Atomic model, Database references, Derived calculations, Non-polymer description, Structure summary, Version format compliance
• Version 1.2: 2017-11-01
  Changes: Refinement description