2P83

Potent and selective isophthalamide S2 hydroxyethylamine inhibitor of BACE1

• PDB DOI: https://doi.org/10.2210/pdb2P83/pdb

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


• Deposited: 2007-03-21 Released: 2007-06-19 
• Deposition Author(s): Benson, T.E., Prince, D.B., Tomasselli, A.G., Emmons, T.L., Paddock, D.J.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free: 0.242 
• R-Value Work: 0.207 

Literature

Potent and selective isophthalamide S(2) hydroxyethylamine inhibitors of BACE1.

Kortum, S.W., Benson, T.E., Bienkowski, M.J., Emmons, T.L., Prince, D.B., Paddock, D.J., Tomasselli, A.G., Moon, J.B., Laborde, A., Tenbrink, R.E.

(2007) Bioorg Med Chem Lett 17: 3378-3383

• PubMed: 17434734 
• DOI: https://doi.org/10.1016/j.bmcl.2007.03.096
• Primary Citation of Related Structures:  
  2P83


• PubMed Abstract: 
  

  The design and synthesis of a novel series of potent BACE1 hydroxyethylamine inhibitors. These inhibitors feature hydrogen bonding substituents at the C-5 position of the isophthalamide ring with improved selectivity over cathepsin D.

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Organizational Affiliation: 

Pfizer Global Research and Development, Pfizer Inc., St. Louis Laboratories, 700 Chesterfield Parkway West, Chesterfield, MO 63017, USA. [e-mail]

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly 2  

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

Biological assembly 2 assigned by authors.

Biological Assembly 3  

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

Biological assembly 3 assigned by authors.

Macromolecule Content

• Total Structure Weight: 152.96 kDa 
• Atom Count: 9,104 
• Modelled Residue Count: 1,116 
• Deposited Residue Count: 1,365 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Beta-secretase 1	A, B, C	455	Homo sapiens	Mutation(s): 0  Gene Names: BACE1, BACE 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
MR0	F [auth A], H [auth B], J [auth C]	N~3~-{(1S,2R)-1-(3,5-DIFLUOROBENZYL)-2-HYDROXY-3-[(3-METHOXYBENZYL)AMINO]PROPYL}-N~1~,N~1~-DIPROPYLBENZENE-1,3,5-TRICARBOXAMIDE C33 H40 F2 N4 O5 XIQAKRFMIYGAIR-XZWHSSHBSA-N
PO4	D [auth A], E [auth A], G [auth B], I [auth C]	PHOSPHATE ION O4 P NBIIXXVUZAFLBC-UHFFFAOYSA-K

Binding Affinity Annotations
ID	Source	Binding Affinity
MR0	BindingDB:  2P83	IC50: 11 (nM) from 1 assay(s)
	PDBBind:  2P83	IC50: 11 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free: 0.242 
• R-Value Work: 0.207 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 81.96	α = 90
b = 103.35	β = 104.12
c = 101.01	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
CNS	refinement
PDB_EXTRACT	data extraction
HKL-2000	data reduction
X-PLOR	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2007-06-19 
Deposition Author(s): Benson, T.E., Prince, D.B., Tomasselli, A.G., Emmons, T.L., Paddock, D.J.

Revision History  

• Version 1.0: 2007-06-19
  Type: Initial release
  
• Version 1.1: 2007-10-16
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2017-10-18
  Changes: Refinement description
• Version 1.4: 2024-10-30
  Changes: Data collection, Database references, Structure summary