4L7H

Diethylaminosulfur Trifluoride-Mediated Intramolecular Cyclization of 2-hydroxy-benzylureas to Fused Bicyclic Aminooxazoline Compounds and Evaluation of Their Biochemical Activity Against Beta-Secretase-1 (BACE-1)

• PDB DOI: https://doi.org/10.2210/pdb4L7H/pdb

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


• Deposited: 2013-06-13 Released: 2013-09-18 
• Deposition Author(s): Huestis, M.P., Liu, W., Volgraf, M., Purkey, H.E., Wang, W., Yu, C., Wu, P., Smith, D., Vigers, G., Dutcher, D., Geck Do, M.K., Hunt, K.W., Siu, M.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.85 Å
• R-Value Free: 0.227 
• R-Value Work: 0.187 
• R-Value Observed: 0.189 

Starting Model: experimental

Literature

Diethylaminosulfur Trifluoride-Mediated Intramolecular Cyclization of 2-hydroxycycloalkylureas to Fused Bicyclic Aminooxazoline Compounds and Evaluation of Their Biochemical Activity Against β-Secretase-1 (BACE-1)

Huestis, M.P., Liu, W., Volgraf, M., Purkey, H., Yu, C., Wang, W., Smith, D., Vigers, G., Dutcher, D., Hunt, K.W., Siu, M.

(2013) Tetrahedron Lett 

• DOI: https://doi.org/10.1016/j.tetlet.2013.07.136

Biological Assembly 1  

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

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

Macromolecule Content

• Total Structure Weight: 46.1 kDa 
• Atom Count: 3,184 
• Modelled Residue Count: 374 
• Deposited Residue Count: 409 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Beta-secretase 1	A	409	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 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
1W1	B [auth A]	2-[(3aR,7aR)-2-amino-7a-(2,4-difluorophenyl)-3a,6,7,7a-tetrahydro[1,3]oxazolo[5,4-c]pyridin-5(4H)-yl]pyridine-3-carbonitrile C18 H15 F2 N5 O RDCJBIHDYIOWEV-CRAIPNDOSA-N
DMS	D [auth A]	DIMETHYL SULFOXIDE C2 H6 O S IAZDPXIOMUYVGZ-UHFFFAOYSA-N
ACT	C [auth A]	ACETATE ION C2 H3 O2 QTBSBXVTEAMEQO-UHFFFAOYSA-M

Binding Affinity Annotations
ID	Source	Binding Affinity
1W1	PDBBind:  4L7H	IC50: 2.00e+5 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.85 Å
• R-Value Free: 0.227 
• R-Value Work: 0.187 
• R-Value Observed: 0.189 
• Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 73.062	α = 90
b = 104.679	β = 94.97
c = 49.995	γ = 90

Software Package:

Software Name	Purpose
HKL-2000	data collection
PHASER	phasing
PHENIX	refinement
DENZO	data reduction
SCALEPACK	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2013-09-18 
Deposition Author(s): Huestis, M.P., Liu, W., Volgraf, M., Purkey, H.E., Wang, W., Yu, C., Wu, P., Smith, D., Vigers, G., Dutcher, D., Geck Do, M.K., Hunt, K.W., Siu, M.

Revision History  

• Version 1.0: 2013-09-18
  Type: Initial release
  
• Version 1.1: 2023-09-20
  Changes: Data collection, Database references, Derived calculations, Refinement description
• Version 1.2: 2024-11-20
  Changes: Structure summary