Biological Assembly 1  

 3D View: Structure | Electron Density | Validation Report

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

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly 2  

 3D View: Structure | Electron Density | Validation Report

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

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 98.47 kDa 
• Atom Count: 6500 
• Modelled Residue Count: 761 
• Deposited Residue Count: 880 
• Unique protein chains: 2

4DVF

Crystal structure of BACE1 with its inhibitor

• DOI: 10.2210/pdb4DVF/pdb

• Classification: HYDROLASE/HYDROLASE INHIBITOR
• Organism(s): Homo sapiens, synthetic construct
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2012-02-23 Released: 2013-01-16 
• Deposition Author(s): Xu, Y.C., Chen, W.Y., Li, L., Chen, T.T.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 0.238 
• R-Value Work: 0.207 
• R-Value Observed: 0.208 

Literature

Cyanobacterial Peptides as a Prototype for the Design of Potent beta-Secretase Inhibitors and the Development of Selective Chemical Probes for Other Aspartic Proteases

Liu, Y., Zhang, W., Li, L., Salvador, L.A., Chen, T.T., Chen, W.Y., Felsenstein, K.M., Ladd, T.B., Price, A.R., Golde, T.E., He, J., Xu, Y.C., Li, Y., Luesch, H.

(2012) J Med Chem 55: 10749-10765

• PubMed: 23181502 
• DOI: 10.1021/jm301630s
• Primary Citation of Related Structures:  
  3UQP, 3UQR, 4DV9, 4DVF, 4FGX


• PubMed Abstract: 
  

Inspired by marine cyanobacterial natural products, we synthesized modified peptides with a central statine-core unit, characteristic for aspartic protease inhibition. A series of tasiamide B analogues inhibited BACE1, a therapeutic target in Alzheimer's disease. We probed the stereospecificity of target engagement and determined additional structure-activity relationships with respect to BACE1 and related aspartic proteases, cathepsins D and E. We cocrystallized selected inhibitors with BACE1 to reveal the structural basis for the activity. Hybrid molecules that combine features of tasiamide B and an isophthalic acid moiety-containing sulfonamide showed nanomolar cellular activity. Compounds were screened in a series of rigorous complementary cell-based assays. We measured secreted APP ectodomain (sAPPβ), membrane bound carboxyl terminal fragment (CTF), levels of β-amyloid (Aβ) peptides and selectivity for β-secretase (BACE1) over γ-secretase. Prioritized compounds showed reasonable stability in vitro and in vivo, and our most potent inhibitor showed efficacy in reducing Aβ levels in the rodent brain.

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Organizational Affiliation: 

Department of Medicinal Chemistry, University of Florida, Gainesville, Florida 32610, United States.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Beta-secretase 1	A, B	433	Homo sapiens	Mutation(s): 2  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

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
METHYL (2S)-1-[(2R,5S,8S,12S,13S)-2,13-DIBENZYL-12-HYDROXY-3,5-DIMETHYL-8-(2-METHYLPROPYL)-15-(3-[(METHYLSULFONYL)AMINO]-5-{[(1R)-1-PHENYLETHYL]CARBAMOYL}PHENYL)-4,7,10,15-TETRAOXO-3,6,9,14-TETRAAZAPENTADECAN-1-OYL]PYRROLIDINE-2-CARBOXYLATE	C, D	7	synthetic construct	Mutation(s): 0

Small Molecules

Modified Residues  2 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
PLJ	C, D	L-PEPTIDE LINKING	C6 H11 N O2		PRO
PSA	C, D	PEPTIDE-LIKE	C11 H15 N O3		PHE

Biologically Interesting Molecules (External Reference) 1 Unique

Entity ID: 2
ID	Chains	Name	Type/Class	2D Diagram	3D Interactions
PRD_000899	C, D	METHYL (2S)-1-[(2R,5S,8S,12S,13S)-2,13-DIBENZYL-12-HYDROXY-3,5-DIMETHYL-8-(2-METHYLPROPYL)-15-(3-[(METHYLSULFONYL)AMINO]-5-{[(1R)-1-PHENYLETHYL]CARBAMOYL}PHENYL)-4,7,10,15-TETRAOXO-3,6,9,14-TETRAAZAPENTADECAN-1-OYL]PYRROLIDINE-2-CARBOXYLATE	Polypeptide / Enzyme inhibitor		Ligand Interaction

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 0.238 
• R-Value Work: 0.207 
• R-Value Observed: 0.208 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 59.568	α = 90
b = 85.822	β = 90
c = 176.654	γ = 90

Software Package:

Software Name	Purpose
SCALA	data scaling
PHASER	phasing
PHENIX	refinement
PDB_EXTRACT	data extraction
ADSC	data collection
HKL-2000	data reduction

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2012-02-23 
• Released Date: 2013-01-16 
Deposition Author(s): Xu, Y.C., Chen, W.Y., Li, L., Chen, T.T.

Revision History  

• Version 1.0: 2013-01-16
  Type: Initial release
  
• Version 1.1: 2021-09-15
  Changes: Database references, Derived calculations, Source and taxonomy