5V0N | pdb_00005v0n

BACE1 in complex with inhibitor 5g

• PDB DOI: https://doi.org/10.2210/pdb5V0N/pdb

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


• Deposited: 2017-02-28 Released: 2017-05-03 
• Deposition Author(s): Mesecar, A., Ghosh, A., Yen, Y.-C.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.15 Å
• R-Value Free: 
  0.202 (Depositor), 0.210 (DCC) 
• R-Value Work: 
  0.161 (Depositor), 0.169 (DCC) 
• R-Value Observed: 
  0.162 (Depositor) 

Starting Model: experimental

Literature

Design, synthesis, and X-ray structural studies of BACE-1 inhibitors containing substituted 2-oxopiperazines as P1'-P2' ligands.

Ghosh, A.K., Brindisi, M., Yen, Y.C., Cardenas, E.L., Ella-Menye, J.R., Kumaragurubaran, N., Huang, X., Tang, J., Mesecar, A.D.

(2017) Bioorg Med Chem Lett 27: 2432-2438

• PubMed: 28427814 
• DOI: https://doi.org/10.1016/j.bmcl.2017.04.011
• Primary Citation Related Structures: 
  5V0N


• PubMed Abstract: 
  

  We report the design and synthesis of a series of BACE1 inhibitors incorporating mono- and bicyclic 6-substituted 2-oxopiperazines as novel P1' and P2' ligands and isophthalamide derivative as P2-P3 ligands. Among mono-substituted 2-oxopiperazines, inhibitor 5a with N-benzyl-2-oxopiperazine and isophthalamide showed potent BACE1 inhibitory activity (K _i =2nM). Inhibitor 5g, with N-benzyl-2-oxopiperazine and substituted indole-derived P2-ligand showed a reduction in potency. The X-ray crystal structure of 5g-bound BACE1 was determined and used to design a set of disubstituted 2-oxopiperazines and bicyclic derivatives that were subsequently investigated. Inhibitor 6j with an oxazolidinone derivative showed a BACE1 inhibitory activity of 23nM and cellular EC ₅₀ of 80nM.

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Organizational Affiliation: 
• Department of Chemistry, Purdue University, West Lafayette, IN 47907, United States; Department of Medicinal Chemistry, Purdue University, West Lafayette, IN 47907, United States. Electronic address: [e-mail].
Department of Chemistry, Purdue University, West Lafayette, IN 47907, United States.
Department of Biological Sciences, Purdue University, West Lafayette, IN 47907, United States.
Protein Studies Program, Oklahoma Medical Research Foundation, United States.
Protein Studies Program, Oklahoma Medical Research Foundation, United States; Department of Biochemistry and Molecular Biology, University of Oklahoma Health Science Center, Oklahoma City, OK 73104, United States.
Department of Chemistry, Purdue University, West Lafayette, IN 47907, United States; Department of Biological Sciences, Purdue University, West Lafayette, IN 47907, United States; Department of Biochemistry, Purdue University, West Lafayette, IN 47907, United States.

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: 149.76 kDa 
• Atom Count: 9,715 
• Modeled Residue Count: 1,121 
• Deposited Residue Count: 1,323 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Beta-secretase 1	A, B, C	441	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 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
8W4	G [auth A], N [auth B], T [auth C]	N-{(1S,2S)-1-[(2S)-4-benzyl-3-oxopiperazin-2-yl]-1-hydroxy-3-phenylpropan-2-yl}-7-ethyl-1,3,3-trimethyl-2,2-dioxo-1,2,3,4-tetrahydro-2lambda~6~-[1,2,5]thiadiazepino[3,4,5-hi]indole-9-carboxamide C36 H43 N5 O5 S WBWSVNAKBNLSOJ-WXWREJFYSA-N
SO4	D [auth A], E [auth A], F [auth A], I [auth B], J [auth B], K [auth B], L [auth B], P [auth C], Q [auth C], R [auth C], S [auth C]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
GOL	M [auth B]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
URE	H [auth A], O [auth B]	UREA C H4 N2 O XSQUKJJJFZCRTK-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
8W4	BindingDB:  5V0N	Ki: 67 (nM) from 1 assay(s)
		EC50: 19 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.15 Å
• R-Value Free:  0.202 (Depositor), 0.210 (DCC) 
• R-Value Work:  0.161 (Depositor), 0.169 (DCC) 
• R-Value Observed: 0.162 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 82.04	α = 90
b = 103.545	β = 104.59
c = 99.765	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
MOSFLM	data reduction
SCALA	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2017-05-03 
Deposition Author(s): Mesecar, A., Ghosh, A., Yen, Y.-C.

Revision History  

• Version 1.0: 2017-05-03
  Type: Initial release
  
• Version 1.1: 2017-05-24
  Changes: Database references
• Version 1.2: 2023-10-04
  Changes: Data collection, Database references, Refinement description
• Version 1.3: 2024-11-20
  Changes: Structure summary