2VNM

Human BACE-1 in complex with 3-(1,1-dioxidotetrahydro-2H-1,2-thiazin- 2-yl)-5-(ethylamino)-N-((1S,2R)-2-hydroxy-1-(phenylmethyl)-3-(((3-(trifluoromethyl)phenyl)methyl)amino)propyl)benzamide

• PDB DOI:  https://doi.org/10.2210/pdb2VNM/pdb

• Classification: HYDROLASE
• Organism(s): Homo sapiens
• Expression System: Cricetulus griseus
• Mutation(s): Yes 


• Deposited: 2008-02-05 Released: 2008-05-20 
• Deposition Author(s): Charrier, N., Clarke, B., Cutler, L., Demont, E., Dingwall, C., Dunsdon, R., East, P., Hawkins, J., Howes, C., Hussain, I., Jeffrey, P., Maile, G., Matico, R., Mosley, J., Naylor, A., OBrien, A., Redshaw, S., Rowland, P., Soleil, V., Smith, K.J., Sweitzer, S., Theobald, P., Vesey, D., Walter, D.S., Wayne, G.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.79 Å
• R-Value Free: 0.231 
• R-Value Work: 0.191 
• R-Value Observed: 0.192 

Literature

Second Generation of Hydroxyethylamine Bace-1 Inhibitors: Optimizing Potency and Oral Bioavailability.

Charrier, N., Clarke, B., Cutler, L., Demont, E., Dingwall, C., Dunsdon, R., East, P., Hawkins, J., Howes, C., Hussain, I., Jeffrey, P., Maile, G., Matico, R., Mosley, J., Naylor, A., O'Brien, A., Redshaw, S., Rowland, P., Soleil, V., Smith, K.J., Sweitzer, S., Theobald, P., Vesey, D., Walter, D.S., Wayne, G.

(2008) J Med Chem 51: 3313

• PubMed: 18457381 
• DOI: https://doi.org/10.1021/jm800138h
• Primary Citation of Related Structures:  
  2VNM, 2VNN


• PubMed Abstract: 
  

BACE-1 inhibition has the potential to provide a disease-modifying therapy for the treatment of Alzheimer's disease. Optimization of a first generation of BACE-1 inhibitors led to the discovery of novel hydroxyethylamines (HEAs) bearing a tricyclic nonprime side. These derivatives have nanomolar cell potency and are orally bioavailable.

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Organizational Affiliation: 

Neurology and Gastrointestinal Centre of Excellence for Drug Discovery, GlaxoSmithKline, New Frontiers Park, Harlow, Essex, UK.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors and generated by PQS (software)

Macromolecule Content

• Total Structure Weight: 45 kDa 
• Atom Count: 3,443 
• Modelled Residue Count: 375 
• Deposited Residue Count: 392 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
BETA-SECRETASE 1	A	392	Homo sapiens	Mutation(s): 4  Gene Names: BACE1, BACE, 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
CM8	B [auth A], C [auth A]	N-[(1S,2R)-1-benzyl-2-hydroxy-3-{[3-(trifluoromethyl)benzyl]amino}propyl]-3-(1,1-dioxido-1,2-thiazinan-2-yl)-5-(ethylamino)benzamide C31 H37 F3 N4 O4 S GPMRAYXRPZKTFK-URLMMPGGSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
CM8	Binding MOAD:  2VNM	IC50: 3 (nM) from 1 assay(s)
	BindingDB:  2VNM	IC50: min: 3, max: 7 (nM) from 3 assay(s)
	PDBBind:  2VNM	IC50: 3 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.79 Å
• R-Value Free: 0.231 
• R-Value Work: 0.191 
• R-Value Observed: 0.192 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 47.952	α = 90
b = 76.217	β = 90
c = 104.492	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
DENZO	data reduction
SCALEPACK	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2008-05-20 
Deposition Author(s): Charrier, N., Clarke, B., Cutler, L., Demont, E., Dingwall, C., Dunsdon, R., East, P., Hawkins, J., Howes, C., Hussain, I., Jeffrey, P., Maile, G., Matico, R., Mosley, J., Naylor, A., OBrien, A., Redshaw, S., Rowland, P., Soleil, V., Smith, K.J., Sweitzer, S., Theobald, P., Vesey, D., Walter, D.S., Wayne, G.

Revision History  

• Version 1.0: 2008-05-20
  Type: Initial release
  
• Version 1.1: 2011-05-08
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2019-03-06
  Changes: Data collection, Experimental preparation, Other
• Version 1.4: 2019-04-03
  Changes: Data collection, Source and taxonomy
• Version 1.5: 2019-05-15
  Changes: Data collection, Experimental preparation