5UX4

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

External Resource: Annotation

Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
Domain Annotation: CATH
Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A	SCOP2 Family	Pepsin-like	8066364	4002301	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	Acid proteases	8066365	3001059	SCOP2 (2022-06-29)
B	SCOP2B Superfamily	Acid proteases	8066365	3001059	SCOP2B (2022-06-29)

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
A	Asp_C	e5ux4A1	A: beta barrels	X: cradle loop barrel	H: RIFT-related	T: acid protease	F: Asp_C	ECOD (1.6)
A	Asp_N	e5ux4A2	A: beta barrels	X: cradle loop barrel	H: RIFT-related	T: acid protease	F: Asp_N	ECOD (1.6)
B	Asp_C	e5ux4B2	A: beta barrels	X: cradle loop barrel	H: RIFT-related	T: acid protease	F: Asp_C	ECOD (1.6)
B	Asp_N	e5ux4B1	A: beta barrels	X: cradle loop barrel	H: RIFT-related	T: acid protease	F: Asp_N	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	2.40.70.10	Mainly Beta	Beta Barrel	Cathepsin D, subunit A	domain 1	CATH (4.3.0)
B	2.40.70.10	Mainly Beta	Beta Barrel	Cathepsin D, subunit A	domain 1	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B	PF00026	Eukaryotic aspartyl protease (Asp)	Eukaryotic aspartyl protease	-	Family

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B	Cathepsin D	peptidase activity catalytic activity, acting on a protein hydrolase activity catalytic activity aspartic-type peptidase activity aspartic-type endopeptidase activity endopeptidase activity binding peptide binding	protein localization regulation of localization establishment of protein localization cellular localization regulation of biological process regulation of cellular process regulation of protein localization regulation of establishment of protein localization biological regulation establishment of localization localization regulation of cellular localization cellular macromolecule localization macromolecule localization protein localization regulation of localization establishment of protein localization cellular localization regulation of biological process regulation of cellular process regulation of protein localization regulation of establishment of protein localization biological regulation establishment of localization localization regulation of cellular localization cellular macromolecule localization macromolecule localization cellular process autophagosome assembly catabolic process organelle assembly vacuole organization macroautophagy autophagy autophagosome organization cellular component biogenesis cellular component organization organelle organization cellular component assembly metabolic process cellular component organization or biogenesis process utilizing autophagic mechanism cellular response to nitrogen compound cellular response to stimulus positive regulation of cell communication positive regulation of signal transduction response to stimulus signaling response to peptide hormone positive regulation of biological process regulation of signal transduction insulin receptor signaling pathway regulation of cellular response to insulin stimulus cell surface receptor protein tyrosine kinase signaling pathway cell communication positive regulation of response to stimulus cellular response to endogenous stimulus response to hormone receptor metabolic process signal transduction enzyme-linked receptor protein signaling pathway positive regulation of cellular process cellular response to hormone stimulus positive regulation of cellular response to insulin stimulus regulation of signaling cell surface receptor signaling pathway response to endogenous stimulus regulation of insulin receptor signaling pathway positive regulation of insulin receptor signaling pathway response to oxygen-containing compound cellular response to peptide hormone stimulus response to nitrogen compound cellular response to oxygen-containing compound receptor recycling cellular response to chemical stimulus regulation of response to stimulus response to chemical response to insulin regulation of cell communication insulin receptor recycling macromolecule metabolic process cellular response to insulin stimulus positive regulation of signaling positive regulation of programmed cell death regulation of apoptotic process regulation of programmed cell death cell death positive regulation of apoptotic process apoptotic process programmed cell death primary metabolic process protein catabolic process protein metabolic process macromolecule catabolic process synaptic vesicle endosomal processing transport establishment of localization in cell intracellular transport vesicle-mediated transport endosomal transport vesicle-mediated transport in synapse response to nutrient levels lipoprotein metabolic process lipoprotein catabolic process proteolysis insulin catabolic process insulin metabolic process	membrane-bounded organelle intracellular anatomical structure pigment granule intracellular vesicle intracellular membrane-bounded organelle intracellular organelle melanosome cellular anatomical structure cytoplasmic vesicle organelle cytoplasm vesicle membrane microdomain membrane raft membrane-bounded organelle intracellular anatomical structure pigment granule intracellular vesicle intracellular membrane-bounded organelle intracellular organelle melanosome cellular anatomical structure cytoplasmic vesicle organelle cytoplasm vesicle membrane microdomain membrane raft membrane lytic vacuole vacuole lysosome GABA-ergic synapse synapse cell junction vacuolar membrane lytic vacuole membrane bounding membrane of organelle lysosomal membrane organelle membrane endosome membrane endosome endomembrane system cytoplasmic vesicle membrane vesicle membrane extracellular region extracellular space membrane-enclosed lumen intracellular organelle lumen organelle lumen endosome lumen presynapse presynaptic endosome

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B	IPR001461	Aspartic peptidase A1	Family
A, B	IPR033121	Peptidase family A1 domain	Domain
A, B	IPR033144	Cathepsin D	Family
A, B	IPR021109	Aspartic peptidase domain superfamily	Homologous Superfamily
A, B	IPR001969	Aspartic peptidase, active site	Active Site
A, B	IPR012848	Aspartic peptidase, N-terminal	Domain

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.