5UX4 | pdb_00005ux4

Crystal Structure of Rat Cathepsin D with (5S)-3-(5,6-dihydro-2H-pyran-3-yl)-1-fluoro- 7-(2-fluoropyridin-3-yl)spiro[chromeno[2,3- c]pyridine-5,4'-[1,3]oxazol]-2'-amine

• PDB DOI: https://doi.org/10.2210/pdb5UX4/pdb

• Classification: HYDROLASE
• Organism(s): Rattus norvegicus
• Expression System: Cricetulus griseus
• Mutation(s): No 


• Deposited: 2017-02-22 Released: 2018-06-13 
• Deposition Author(s): Sickmier, A.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.81 Å
• R-Value Free: 
  0.237 (Depositor), 0.236 (DCC) 
• R-Value Work: 
  0.191 (Depositor), 0.191 (DCC) 
• R-Value Observed: 
  0.194 (Depositor) 

Starting Model: experimental

Literature

Development of 2-aminooxazoline 3-azaxanthene beta-amyloid cleaving enzyme (BACE) inhibitors with improved selectivity against Cathepsin D.

Low, J.D., Bartberger, M.D., Chen, K., Cheng, Y., Fielden, M.R., Gore, V., Hickman, D., Liu, Q., Allen Sickmier, E., Vargas, H.M., Werner, J., White, R.D., Whittington, D.A., Wood, S., Minatti, A.E.

(2017) Medchemcomm 8: 1196-1206

• PubMed: 30108829 
• DOI: https://doi.org/10.1039/c7md00106a
• Primary Citation Related Structures: 
  5UX4, 5UYU


• PubMed Abstract: 
  

  As part of an ongoing effort at Amgen to develop a disease-modifying therapy for Alzheimer's disease, we have previously used the aminooxazoline xanthene (AOX) scaffold to generate potent and orally efficacious BACE1 inhibitors. While AOX-BACE1 inhibitors demonstrated acceptable cardiovascular safety margins, a retinal pathological finding in rat toxicological studies demanded further investigation. It has been widely postulated that such retinal toxicity might be related to off-target inhibition of Cathepsin D (CatD), a closely related aspartyl protease. We report the development of AOX-BACE1 inhibitors with improved selectivity against CatD by following a structure- and property-based approach. Our efforts culminated in the discovery of a picolinamide-substituted 3-aza-AOX-BACE1 inhibitor absent of retinal effects in an early screening rat toxicology study.

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Organizational Affiliation: 
• Department of Medicinal Chemistry , Amgen Inc. , One Amgen Center Drive , Thousand Oaks , CA 91320 , USA . Email: [e-mail] ; Tel: [phone].
Department of Molecular Engineering , Amgen Inc. , One Amgen Center Drive , Thousand Oaks , CA 91320 , USA.
Department Discovery Technologies , Amgen Inc. , One Amgen Center Drive , Thousand Oaks , CA 91320 , USA.
Comparative Biology and Safety Sciences , Amgen Inc. , One Amgen Center Drive , Thousand Oaks , CA 91320 , USA.
Department of Pharmacokinetics and Drug Metabolism , Amgen Inc. , One Amgen Center Drive , Thousand Oaks , CA 91320 , USA.
Department of Molecular Engineering , Amgen Inc. , 360 Binney Street , Cambridge , MA 02142 , USA.
Department of Medicinal Chemistry , Amgen Inc. , 360 Binney Street , Cambridge , MA 02142 , USA.
Department of Neuroscience , Amgen Inc. , One Amgen Center Drive , Thousand Oaks , CA 91320 , USA.

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)

Macromolecule Content 

• Total Structure Weight: 95.64 kDa 
• Atom Count: 5,405 
• Modeled Residue Count: 677 
• Deposited Residue Count: 840 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Cathepsin D	A, B	420	Rattus norvegicus	Mutation(s): 0  Gene Names: Ctsd EC: 3.4.23.5
UniProt
Find proteins for P24268 (Rattus norvegicus) Explore P24268  Go to UniProtKB:  P24268
Glycosylation
Glycosylation Sites: 2		Go to GlyGen: P24268-1

Oligosaccharides

Help  

Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	C	2		N-Glycosylation
Glycosylation Resources
GlyTouCan: G42666HT GlyCosmos: G42666HT GlyGen: G42666HT

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
3UT	E [auth A], H [auth B]	(5S)-3-(5,6-dihydro-2H-pyran-3-yl)-1-fluoro-7-(2-fluoropyridin-3-yl)spiro[chromeno[2,3-c]pyridine-5,4'-[1,3]oxazol]-2'-amine C24 H18 F2 N4 O3 JAZOCUNZCUBRJX-DEOSSOPVSA-N
NAG	D [auth A], F [auth B], G [auth B]	2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.81 Å
• R-Value Free:  0.237 (Depositor), 0.236 (DCC) 
• R-Value Work:  0.191 (Depositor), 0.191 (DCC) 
• R-Value Observed: 0.194 (Depositor) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 136.514	α = 90
b = 66.122	β = 99.53
c = 99.555	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2018-06-13 
Deposition Author(s): Sickmier, A.

Revision History  

• Version 1.0: 2018-06-13
  Type: Initial release
  
• Version 1.1: 2018-08-29
  Changes: Data collection, Database references
• Version 2.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Atomic model, Data collection, Derived calculations, Structure summary
• Version 2.1: 2023-10-04
  Changes: Data collection, Database references, Refinement description, Structure summary
• Version 2.2: 2024-11-13
  Changes: Structure summary