3CKR

Crystal structure of BACE-1 in complex with inhibitor

• PDB DOI: https://doi.org/10.2210/pdb3CKR/pdb

• Classification: HYDROLASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2008-03-16 Released: 2008-06-03 
• Deposition Author(s): Min, K.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.70 Å
• R-Value Free: 0.257 
• R-Value Work: 0.251 

Literature

Synthesis, SAR, and X-ray structure of human BACE-1 inhibitors with cyclic urea derivatives

Park, H., Min, K., Kwak, H.-S., Koo, K.D., Lim, D., Seo, S.-W., Choi, J.-U., Platt, B., Choi, D.-Y.

(2008) Bioorg Med Chem Lett 18: 2900-2904

• PubMed: 18434152 
• DOI: https://doi.org/10.1016/j.bmcl.2008.03.081
• Primary Citation of Related Structures:  
  3CKP, 3CKR


• PubMed Abstract: 
  

  We describe synthesis and evaluation of a series of cyclic urea derivatives with hydroxylethylamine isostere. Modification of P3, P1, and P2' and combination of SAR display a >100-fold increase in potency with good cellular activity (IC(50)=0.15microM) relative to the previously reported compound 3.

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Organizational Affiliation: 

Drug Discovery, Research & Development, LG Life Sciences, 104-1 Munji-dong, Yuseong-gu, Daejon 305-380, Republic of Korea. [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: 139.59 kDa 
• Atom Count: 9,135 
• Modelled Residue Count: 1,133 
• Deposited Residue Count: 1,236 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Beta-secretase 1	A, B, C	412	Homo sapiens	Mutation(s): 2  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
009	D [auth A], E [auth B], F [auth C]	(4S)-1,4-dibenzyl-N-[(1S,2R)-1-benzyl-3-{[3-(dimethylamino)benzyl]amino}-2-hydroxypropyl]-2-oxoimidazolidine-4-carboxamide C37 H43 N5 O3 DCJGHBWTJFHQCR-UEHMVRIRSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
009	BindingDB:  3CKR	Ki: 5001 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.70 Å
• R-Value Free: 0.257 
• R-Value Work: 0.251 
• Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 224.457	α = 90
b = 108.126	β = 100.87
c = 61.135	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2008-06-03 
Deposition Author(s): Min, K.

Revision History  

• Version 1.0: 2008-06-03
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2017-10-25
  Changes: Refinement description
• Version 1.3: 2021-11-10
  Changes: Database references, Derived calculations