3DM6

Beta-secretase 1 complexed with statine-based inhibitor

• PDB DOI: https://doi.org/10.2210/pdb3DM6/pdb

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


• Deposited: 2008-06-30 Released: 2008-12-16 
• Deposition Author(s): Lindberg, J., Borkakoti, N., Nystrom, S.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.60 Å
• R-Value Free: 0.281 
• R-Value Work: 0.223 
• R-Value Observed: 0.226 

Literature

Design, synthesis and SAR of potent statine-based BACE-1 inhibitors: exploration of P1 phenoxy and benzyloxy residues

Back, M., Nyhlen, J., Kvarnstrom, I., Appelgren, S., Borkakoti, N., Jansson, K., Lindberg, J., Nystrom, S., Hallberg, A., Rosenquist, S., Samuelsson, B.

(2008) Bioorg Med Chem 16: 9471-9486

• PubMed: 18842420 
• DOI: https://doi.org/10.1016/j.bmc.2008.09.041
• Primary Citation of Related Structures:  
  3DM6


• PubMed Abstract: 
  

  Several BACE-1 inhibitors with low nanomolar level activities, encompassing a statine-based core structure with phenyloxymethyl- and benzyloxymethyl residues in the P1 position, are presented. The novel P1 modification introduced to allow the facile exploration of the S1 binding pocket of BACE-1, delivered highly promising inhibitors.

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Organizational Affiliation: 

Department of Chemistry, Linköping University, S-58183 Linköping, Sweden.

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: 139.01 kDa 
• Atom Count: 8,934 
• Modelled Residue Count: 1,104 
• Deposited Residue Count: 1,218 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Beta-secretase 1	A, B, C	406	Homo sapiens	Mutation(s): 0  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
757	D [auth A], F [auth B], H [auth C]	5-[[(2S)-2-[[(3R,4S)-5-(3,5-difluorophenoxy)-3-hydroxy-4-[[3-(methyl-methylsulfonyl-amino)-5-[[(1R)-1-phenylethyl]carbamoyl]phenyl]carbonylamino]pentanoyl]amino]-3-methyl-butanoyl]amino]benzene-1,3-dicarboxylic acid C42 H45 F2 N5 O12 S XYKCBRCSBVZGIL-WRXYKUNKSA-N
IPA	E [auth A], G [auth B], I [auth C]	ISOPROPYL ALCOHOL C3 H8 O KFZMGEQAYNKOFK-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
757	BindingDB:  3DM6	IC50: 37 (nM) from 1 assay(s)
	PDBBind:  3DM6	IC50: 37 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.60 Å
• R-Value Free: 0.281 
• R-Value Work: 0.223 
• R-Value Observed: 0.226 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 83.435	α = 90
b = 103.017	β = 103.5
c = 103.11	γ = 90

Software Package:

Software Name	Purpose
MOSFLM	data reduction
SCALA	data scaling
PHASER	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction

Structure Validation

Entry History 

Deposition Data

• Released Date: 2008-12-16 
Deposition Author(s): Lindberg, J., Borkakoti, N., Nystrom, S.

Revision History  

• Version 1.0: 2008-12-16
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance