4L7G

Diethylaminosulfur Trifluoride-Mediated Intramolecular Cyclization of 2-hydroxy-benzylureas to Fused Bicyclic Aminooxazoline Compounds and Evaluation of Their Biochemical Activity Against Beta-Secretase-1 (BACE1)

PDB DOI: https://doi.org/10.2210/pdb4L7G/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., Wang, W., Yu, C., Wu, P., Smith, D., Vigers, G., Dutcher, D., Geck Do, M.K., Hunt, K.W., Siu, M.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.38 Å
R-Value Free: 0.192
R-Value Work: 0.154
R-Value Observed: 0.156

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.2 of the entry. See complete history.

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

Macromolecule Content

Total Structure Weight: 45.98 kDa
Atom Count: 3,486
Modelled Residue Count: 373
Deposited Residue Count: 409
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

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
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P56817
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
1W0 Query on 1W0 Download Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A] mmCIF format, chain B [auth A]	B [auth A]	(3aS,7aR)-7a-[3-(pyrimidin-5-yl)phenyl]-3a,6,7,7a-tetrahydro-4H-pyrano[4,3-d][1,3]oxazol-2-amine C₁₆ H₁₆ N₄ O₂ QBOAOWFKBWILHE-GDBMZVCRSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]
DMS Query on DMS Download Ideal Coordinates CCD File SDF format, chain C [auth A] MOL2 format, chain C [auth A] mmCIF format, chain C [auth A]	C [auth A]	DIMETHYL SULFOXIDE C₂ H₆ O S IAZDPXIOMUYVGZ-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]

Binding Affinity Annotations
ID	Source	Binding Affinity
1W0	PDBBind: 4L7G	IC50: 9.93e+4 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.38 Å
R-Value Free: 0.192
R-Value Work: 0.154
R-Value Observed: 0.156
Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 72.664	α = 90
b = 104.471	β = 94.82
c = 50.076	γ = 90

Software Package:

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

Structure Validation

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Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2013-09-18

Deposition Author(s):

Revision History (Full details and data files)

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: 2024-10-16
Changes: Structure summary