3N3G

4-(3-Trifluoromethylphenyl)-pyrimidine-2-carbonitrile as cathepsin S inhibitors: N3, not N1 is critically important

External Resource: Annotation

Domain Annotation: SCOP/SCOPe Classification
Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
Domain Annotation: CATH
Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification
Pharos: Disease Associations

Domain Annotation: SCOP/SCOPe Classification SCOP-e Database Homepage

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
A	d3n3ga_	Alpha and beta proteins (a+b)	Cysteine proteinases	Cysteine proteinases	Papain-like	(Pro)cathepsin S	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
B	d3n3gb_	Alpha and beta proteins (a+b)	Cysteine proteinases	Cysteine proteinases	Papain-like	(Pro)cathepsin S	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A	SCOP2B Superfamily	Cysteine proteinases	8042180	3001808	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Cysteine proteinases	8042180	3001808	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	Peptidase_C1	e3n3gA1	A: a+b complex topology	X: Cysteine proteinases-like	H: Cysteine proteinases (From Topology)	T: Cysteine proteinases	F: Peptidase_C1	ECOD (1.6)
B	Peptidase_C1	e3n3gB1	A: a+b complex topology	X: Cysteine proteinases-like	H: Cysteine proteinases (From Topology)	T: Cysteine proteinases	F: Peptidase_C1	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	3.90.70.10	Alpha Beta	Alpha-Beta Complex	Cathepsin B	Chain A	CATH (4.3.0)
B	3.90.70.10	Alpha Beta	Alpha-Beta Complex	Cathepsin B	Chain A	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B	PF00112	Papain family cysteine protease (Peptidase_C1)	Papain family cysteine protease	-	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B	Cathepsin S	cysteine-type peptidase activity peptidase activity catalytic activity, acting on a protein cysteine-type endopeptidase activity hydrolase activity catalytic activity endopeptidase activity serine hydrolase activity serine-type peptidase activity serine-type endopeptidase activity collagen binding protein-containing complex binding binding extracellular matrix binding cysteine-type peptidase activity peptidase activity catalytic activity, acting on a protein cysteine-type endopeptidase activity hydrolase activity catalytic activity endopeptidase activity serine hydrolase activity serine-type peptidase activity serine-type endopeptidase activity collagen binding protein-containing complex binding binding extracellular matrix binding protein binding laminin binding enzyme regulator activity enzyme activator activity peptidase regulator activity molecular function activator activity cysteine-type endopeptidase activator activity involved in apoptotic process molecular function regulator activity cysteine-type endopeptidase regulator activity involved in apoptotic process peptidase activator activity peptidase activator activity involved in apoptotic process fibronectin binding proteoglycan binding carbohydrate derivative binding	collagen catabolic process catabolic process metabolic process cellular process collagen metabolic process regulation of localization positive regulation of cation transmembrane transport regulation of cellular process transport monoatomic ion transmembrane transport positive regulation of biological process regulation of transmembrane transporter activity regulation of monoatomic ion transmembrane transport regulation of transporter activity collagen catabolic process catabolic process metabolic process cellular process collagen metabolic process regulation of localization positive regulation of cation transmembrane transport regulation of cellular process transport monoatomic ion transmembrane transport positive regulation of biological process regulation of transmembrane transporter activity regulation of monoatomic ion transmembrane transport regulation of transporter activity monoatomic cation transmembrane transport localization positive regulation of molecular function positive regulation of monoatomic ion transport positive regulation of transmembrane transport monoatomic ion transport positive regulation of monoatomic ion transmembrane transport monoatomic cation transport positive regulation of cellular process regulation of monoatomic ion transmembrane transporter activity regulation of biological process regulation of transport regulation of monoatomic ion transport biological regulation positive regulation of cation channel activity establishment of localization regulation of cation channel activity transmembrane transport regulation of molecular function regulation of transmembrane transport positive regulation of transport positive regulation of transporter activity positive regulation of ion transmembrane transporter activity regulation of monoatomic cation transmembrane transport response to stimulus immune response immune system process adaptive immune response cellular response to stimulus positive regulation of cell communication positive regulation of signal transduction signaling regulation of signal transduction regulation of programmed cell death positive regulation of apoptotic signaling pathway cell communication positive regulation of response to stimulus signal transduction regulation of signaling positive regulation of programmed cell death regulation of apoptotic process cell death positive regulation of apoptotic process apoptotic signaling pathway regulation of response to stimulus regulation of cell communication apoptotic process programmed cell death positive regulation of signaling regulation of apoptotic signaling pathway proteolysis involved in protein catabolic process proteolysis primary metabolic process protein catabolic process protein metabolic process macromolecule metabolic process macromolecule catabolic process antigen processing and presentation of exogenous peptide antigen via MHC class II antigen processing and presentation antigen processing and presentation of peptide or polysaccharide antigen via MHC class II antigen processing and presentation of peptide antigen via MHC class II antigen processing and presentation of exogenous peptide antigen antigen processing and presentation of peptide antigen antigen processing and presentation of exogenous antigen cellular component organization cellular component disassembly extracellular matrix disassembly basement membrane disassembly extracellular matrix organization cellular component organization or biogenesis extracellular structure organization external encapsulating structure organization basement membrane organization gene expression macromolecule biosynthetic process protein maturation biosynthetic process protein processing response to thyroid hormone response to endogenous stimulus cellular response to endogenous stimulus cellular response to chemical stimulus response to hormone response to chemical cellular response to thyroid hormone stimulus cellular response to hormone stimulus response to pH response to abiotic stimulus response to acidic pH regulation of defense response positive regulation of response to biotic stimulus regulation of response to biotic stimulus biological process involved in interspecies interaction between organisms pattern recognition receptor signaling pathway regulation of response to external stimulus toll-like receptor signaling pathway response to biotic stimulus immune response-activating signaling pathway positive regulation of response to external stimulus immune response-regulating signaling pathway positive regulation of immune response regulation of response to stress response to stress innate immune response regulation of immune system process response to external biotic stimulus positive regulation of immune system process innate immune response-activating signaling pathway positive regulation of innate immune response defense response response to other organism regulation of innate immune response defense response to symbiont response to external stimulus defense response to other organism positive regulation of defense response activation of innate immune response regulation of immune response activation of immune response	membrane-bounded organelle intracellular anatomical structure lytic vacuole membrane-enclosed lumen vacuolar lumen vacuole intracellular membrane-bounded organelle lysosomal lumen intracellular organelle lumen intracellular organelle cellular anatomical structure organelle lumen organelle cytoplasm membrane-bounded organelle intracellular anatomical structure lytic vacuole membrane-enclosed lumen vacuolar lumen vacuole intracellular membrane-bounded organelle lysosomal lumen intracellular organelle lumen intracellular organelle cellular anatomical structure organelle lumen organelle cytoplasm lysosome cell periphery extracellular matrix external encapsulating structure collagen-containing extracellular matrix intracellular vesicle endomembrane system endolysosome cytoplasmic vesicle endosome lumen vesicle endosome endolysosome lumen phagocytic vesicle endocytic vesicle ficolin-1-rich granule ficolin-1-rich granule lumen secretory granule secretory vesicle tertiary granule lumen tertiary granule extracellular region late endosome extracellular space

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B	IPR025661	Cysteine peptidase, asparagine active site	Active Site
A, B	IPR000169	Cysteine peptidase, cysteine active site	Active Site
A, B	IPR038765	Papain-like cysteine peptidase superfamily	Homologous Superfamily
A, B	IPR013128	Peptidase C1A	Family
A, B	IPR000668	Peptidase C1A, papain C-terminal	Domain
A, B	IPR013201	Cathepsin propeptide inhibitor domain (I29)	Domain
A, B	IPR025660	Cysteine peptidase, histidine active site	Active Site
A, B	IPR039417	Papain-like cysteine endopeptidase	Domain

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
A, B	Pharos: P25774	Neoplasm Invasiveness obesity disorder contact dermatitis malignant glioma pancreatic intraductal papillary-mucinous neoplasm Barrett esophagus pilocytic astrocytoma rheumatoid arthritis cystic fibrosis subependymal giant cell astrocytoma glioblastoma interstitial cystitis malignant colon neoplasm malignant pancreatic neoplasm nephrosclerosis Neoplasm Invasiveness obesity disorder contact dermatitis malignant glioma pancreatic intraductal papillary-mucinous neoplasm Barrett esophagus pilocytic astrocytoma rheumatoid arthritis cystic fibrosis subependymal giant cell astrocytoma glioblastoma interstitial cystitis malignant colon neoplasm malignant pancreatic neoplasm nephrosclerosis osteosarcoma pancreatic intraductal papillary-mucinous neoplasm with low grade dysplasia plasma cell myeloma Crohn disease Sjogren syndrome diabetes mellitus tuberculosis heart disease invasive ductal breast carcinoma lung cancer malignant ependymoma MALT lymphoma non-small cell lung carcinoma ovarian cancer periodontitis prostate carcinoma cutaneous lupus erythematosus skin basal cell carcinoma esophageal adenocarcinoma IgA glomerulonephritis juvenile dermatomyositis lung carcinoma

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.