4I0J | pdb_00004i0j

SPR and structural analysis yield insight towards mechanism of inhibition of BACE inhibitors

• PDB DOI: https://doi.org/10.2210/pdb4I0J/pdb

• Classification: hydrolase/hydrolase inhibitor
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2012-11-16 Released: 2013-03-06 
• Deposition Author(s): Yao, N., Brecht, E.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.99 Å
• R-Value Free: 
  0.295 (Depositor), 0.295 (DCC) 
• R-Value Work: 
  0.226 (Depositor), 0.229 (DCC) 
• R-Value Observed: 
  0.229 (Depositor) 

Literature

SPR and structural analysis yield insight towards mechanism of inhibition of BACE inhibitors

Mondal, K., Regnstrom, K., Morishige, W., Barbour, R., Beroza, P., Yao, N., Bova, M.P.

To be published.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly 2  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 2 generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 46.19 kDa 
• Atom Count: 3,327 
• Modeled Residue Count: 388 
• Deposited Residue Count: 406 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Beta-secretase 1	A	406	Homo sapiens	Mutation(s): 0  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 GTEx:  ENSG00000186318

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
842	F [auth A]	N-[(1S,2R)-1-(3,5-difluorobenzyl)-2-hydroxy-3-({1-[3-(1H-pyrazol-1-yl)phenyl]cyclohexyl}amino)propyl]acetamide C27 H32 F2 N4 O2 QXNFPOMRKODYSK-IZZNHLLZSA-N
ZN	B [auth A], C [auth A], D [auth A], E [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.99 Å
• R-Value Free:  0.295 (Depositor), 0.295 (DCC) 
• R-Value Work:  0.226 (Depositor), 0.229 (DCC) 
• R-Value Observed: 0.229 (Depositor) 

Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 75.228	α = 90
b = 104.039	β = 90
c = 99.063	γ = 90

Software Package:

Software Name	Purpose
StructureStudio	data collection
MOLREP	phasing
REFMAC	refinement

Structure Validation

Entry History 

Deposition Data

• Released Date: 2013-03-06 
Deposition Author(s): Yao, N., Brecht, E.

Revision History  

• Version 1.0: 2013-03-06
  Type: Initial release
  
• Version 1.1: 2024-11-20
  Changes: Data collection, Database references, Derived calculations, Structure summary