3K5D

Crystal Structure of BACE-1 in complex with AHM178

• PDB DOI: https://doi.org/10.2210/pdb3K5D/pdb

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


• Deposited: 2009-10-07 Released: 2010-05-05 
• Deposition Author(s): Rondeau, J.-M.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.90 Å
• R-Value Free: 0.238 
• R-Value Work: 0.202 
• R-Value Observed: 0.204 

Literature

Structure-based design and synthesis of novel P2/P3 modified, non-peptidic beta-secretase (BACE-1) inhibitors.

Hanessian, S., Shao, Z., Betschart, C., Rondeau, J.M., Neumann, U., Tintelnot-Blomley, M.

(2010) Bioorg Med Chem Lett 20: 1924-1927

• PubMed: 20172717 
• DOI: https://doi.org/10.1016/j.bmcl.2010.01.139
• Primary Citation of Related Structures:  
  3K5D, 3K5F, 3K5G


• PubMed Abstract: 
  

  Starting from peptidomimetic BACE-1 inhibitors, the P2 amino acid including the P2/P3 peptide bond was replaced by a rigid 3-aminomethyl cyclohexane carboxylic acid. Co-crystallization revealed an unexpected binding mode with the P3/P4 amide bond placed into the S3 pocket resulting in a new hydrogen bond interaction pattern. Further optimization based on this structure resulted in highly potent BACE-1 inhibitors with selectivity over BACE-2 and cathepsin D.

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Organizational Affiliation: 

Department of Chemistry, Université de Montréal, Montréal, Canada. [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: 137.94 kDa 
• Atom Count: 9,049 
• Modelled Residue Count: 1,126 
• Deposited Residue Count: 1,224 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Beta-secretase 1	A, B, C	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 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
XLI	D [auth A], E [auth B], F [auth C]	N-acetyl-L-leucyl-N-[(4S,5S,7R)-8-(butylamino)-5-hydroxy-2,7-dimethyl-8-oxooctan-4-yl]-L-methioninamide C27 H52 N4 O5 S PEWRQHFGBBTOMS-FFYZIMEISA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
XLI	PDBBind:  3K5D	IC50: 53 (nM) from 1 assay(s)
	BindingDB:  3K5D	IC50: 53 (nM) from 1 assay(s)

Biologically Interesting Molecules (External Reference) 1 Unique

Entity ID: 2
ID	Chains	Name	Type/Class	2D Diagram	3D Interactions
PRD_000675 (XLI)	D [auth A], E [auth B], F [auth C]	AHM178	Peptide-like / Enzyme inhibitor

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.90 Å
• R-Value Free: 0.238 
• R-Value Work: 0.202 
• R-Value Observed: 0.204 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 82.547	α = 90
b = 101.299	β = 104.16
c = 102.218	γ = 90

Software Package:

Software Name	Purpose
CNX	refinement
DENZO	data reduction
SCALEPACK	data scaling
CNX	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2010-05-05 
Deposition Author(s): Rondeau, J.-M.

Revision History  

• Version 1.0: 2010-05-05
  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: 2012-12-12
  Changes: Other
• Version 1.3: 2017-11-01
  Changes: Refinement description
• Version 1.4: 2024-11-06
  Changes: Data collection, Database references, Derived calculations, Structure summary