2NTR | pdb_00002ntr

Crystal structure of Human Bace-1 bound to inhibitor

• PDB DOI: https://doi.org/10.2210/pdb2NTR/pdb

• Classification: HYDROLASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): Yes 


• Deposited: 2006-11-08 Released: 2007-11-13 
• Deposition Author(s): Munshi, S.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 
  0.257 (Depositor) 
• R-Value Work: 
  0.228 (Depositor) 

Starting Model: experimental

Literature

Beta-secretase (BACE-1) inhibitors: accounting for 10s loop flexibility using rigid active sites.

McGaughey, G.B., Colussi, D., Graham, S.L., Lai, M.T., Munshi, S.K., Nantermet, P.G., Pietrak, B., Rajapakse, H.A., Selnick, H.G., Stauffer, S.R., Holloway, M.K.

(2007) Bioorg Med Chem Lett 17: 1117-1121

• PubMed: 17112725 
• DOI: https://doi.org/10.1016/j.bmcl.2006.11.003
• Primary Citation Related Structures: 
  2NTR


• PubMed Abstract: 
  

  BACE-1 is a flexible enzyme with experimentally determined motion in the flap region, the catalytic aspartates, and the 10s loop. Four in-house crystallographically determined complexes of tertiary carbinamine inhibitors revealed 10s loop motion in the S(3) pocket. These X-ray structures were used to correlate K(i) values, which span over five orders of magnitude, with the calculated interaction energy, using the Merck Molecular Force Field for a series of 19 tertiary carbinamine inhibitors.

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Organizational Affiliation: 
• Department of Molecular Systems, Merck Research Laboratories, PO Box 4, West Point, PA 19486, USA. [e-mail]

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 45.69 kDa 
• Atom Count: 3,228 
• Modeled Residue Count: 379 
• Deposited Residue Count: 405 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Beta-secretase 1	A	405	Homo sapiens	Mutation(s): 2  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 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
L00	B [auth A]	(2R)-2-(5-{3-chloro-6-((2-methoxyethyl){[(1S,2S)-2-methylcyclopropyl]methyl}amino)-2-[methyl(methylsulfonyl)amino]pyrid in-4-yl}-1,3,4-oxadiazol-2-yl)-1-phenylpropan-2-amine C26 H35 Cl N6 O4 S NIFMMESJJLKLHP-BNJIMDBKSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free:  0.257 (Depositor) 
• R-Value Work:  0.228 (Depositor) 

Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 103.922	α = 90
b = 128.176	β = 90
c = 76.461	γ = 90

Software Package:

Software Name	Purpose
CNX	refinement
HKL-2000	data collection
HKL-2000	data reduction
HKL-2000	data scaling
CNX	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2007-11-13 
Deposition Author(s): Munshi, S.

Revision History  

• Version 1.0: 2007-11-13
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2021-10-20
  Changes: Database references, Derived calculations, Structure summary
• Version 1.3: 2023-08-30
  Changes: Data collection, Refinement description
• Version 1.4: 2024-10-30
  Changes: Structure summary