1TQF

Crystal structure of human Beta secretase complexed with inhibitor

• PDB DOI: https://doi.org/10.2210/pdb1TQF/pdb

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


• Deposited: 2004-06-17 Released: 2004-11-09 
• Deposition Author(s): Munshi, S., Chen, Z., Kuo, L.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 0.256 
• R-Value Work: 0.221 

Starting Model: experimental

Literature

Identification of a small molecule nonpeptide active site beta-secretase inhibitor that displays a nontraditional binding mode for aspartyl proteases.

Coburn, C.A., Stachel, S.J., Li, Y.M., Rush, D.M., Steele, T.G., Chen-Dodson, E., Holloway, M.K., Xu, M., Huang, Q., Lai, M.T., DiMuzio, J., Crouthamel, M.C., Shi, X.P., Sardana, V., Chen, Z., Munshi, S., Kuo, L., Makara, G.M., Annis, D.A., Tadikonda, P.K., Nash, H.M., Vacca, J.P., Wang, T.

(2004) J Med Chem 47: 6117-6119

• PubMed: 15566281 
• DOI: https://doi.org/10.1021/jm049388p
• Primary Citation of Related Structures:  
  1TQF


• PubMed Abstract: 
  

  A small molecule nonpeptide inhibitor of beta-secretase has been developed, and its binding has been defined through crystallographic determination of the enzyme-inhibitor complex. The molecule is shown to bind to the catalytic aspartate residues in an unprecedented manner in the field of aspartyl protease inhibition. Additionally, the complex reveals a heretofore unknown S(3) subpocket that is created by the inhibitor. This structure has served an important role in the design of newer beta-secretase inhibitors.

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Organizational Affiliation: 

Department of Medicinal Chemistry, Merck Research Laoratories, West Point, PA 19486-0004, 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: 3,317 
• Modelled Residue Count: 371 
• 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
32P	B [auth A]	3-{2-[(5-AMINOPENTYL)AMINO]-2-OXOETHOXY}-5-({[1-(4-FLUOROPHENYL)ETHYL]AMINO}CARBONYL)PHENYL PHENYLMETHANESULFONATE C29 H34 F N3 O6 S UUMRCVIXZFKZAU-OAQYLSRUSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
32P	PDBBind:  1TQF	IC50: 1400 (nM) from 1 assay(s)
	BindingDB:  1TQF	IC50: 1400 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 0.256 
• R-Value Work: 0.221 
• Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 104.916	α = 90
b = 128.181	β = 90
c = 76.272	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2004-11-09 
Deposition Author(s): Munshi, S., Chen, Z., Kuo, L.

Revision History  

• Version 1.0: 2004-11-09
  Type: Initial release
  
• Version 1.1: 2007-10-11
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2021-10-27
  Changes: Database references, Derived calculations
• Version 1.4: 2023-08-23
  Changes: Data collection, Refinement description
• Version 1.5: 2024-10-16
  Changes: Structure summary