1MHW

Design of non-covalent inhibitors of human cathepsin L. From the 96-residue proregion to optimized tripeptides

External Resource: Annotation

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

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

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
A	d1mhw.1	Alpha and beta proteins (a+b)	Cysteine proteinases	Cysteine proteinases	Papain-like	(Pro)cathepsin L	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
C [auth B]	d1mhw.2	Alpha and beta proteins (a+b)	Cysteine proteinases	Cysteine proteinases	Papain-like	(Pro)cathepsin L	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
B [auth C]	d1mhw.1	Alpha and beta proteins (a+b)	Cysteine proteinases	Cysteine proteinases	Papain-like	(Pro)cathepsin L	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
D	d1mhw.2	Alpha and beta proteins (a+b)	Cysteine proteinases	Cysteine proteinases	Papain-like	(Pro)cathepsin L	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)

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)
C [auth B]	3.90.70.10	Alpha Beta	Alpha-Beta Complex	Cathepsin B	Chain A	CATH (4.3.0)
B [auth C]	2.40.50.170	Mainly Beta	Beta Barrel	OB fold (Dihydrolipoamide Acetyltransferase, E2P)	Cysteine proteinases. Chain C	CATH (4.3.0)
D	2.40.50.170	Mainly Beta	Beta Barrel	OB fold (Dihydrolipoamide Acetyltransferase, E2P)	Cysteine proteinases. Chain C	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, C [auth B]	PF00112	Papain family cysteine protease (Peptidase_C1)	Papain family cysteine protease	-	Domain
B [auth C], D	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
E, F, G, H	4-biphenylacetyl-Cys-(D)Arg-Tyr-N-(2-phenylethyl) amide	-	-	-
A, C [auth B]	Cathepsin L	protein binding binding histone binding serpin family protein binding cysteine-type peptidase activity peptidase activity catalytic activity, acting on a protein hydrolase activity catalytic activity enzyme regulator activity enzyme activator activity peptidase regulator activity molecular function activator activity cysteine-type endopeptidase activator activity involved in apoptotic process protein binding binding histone binding serpin family protein binding cysteine-type peptidase activity peptidase activity catalytic activity, acting on a protein hydrolase activity catalytic activity 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 cysteine-type endopeptidase activity endopeptidase activity collagen binding protein-containing complex binding proteoglycan binding carbohydrate derivative binding	organonitrogen compound metabolic process cellular biosynthetic process cellular metabolic process primary metabolic process gene expression macromolecule biosynthetic process protein maturation organic substance metabolic process protein autoprocessing biosynthetic process proteolysis organic substance biosynthetic process protein processing metabolic process organonitrogen compound metabolic process cellular biosynthetic process cellular metabolic process primary metabolic process gene expression macromolecule biosynthetic process protein maturation organic substance metabolic process protein autoprocessing biosynthetic process proteolysis organic substance biosynthetic process protein processing metabolic process cellular process protein metabolic process macromolecule metabolic process response to stimulus immune response immune system process adaptive immune response cellular response to stimulus positive regulation of cell communication regulation of cellular process positive regulation of signal transduction signaling positive regulation of biological process 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 positive regulation of cellular process regulation of biological process regulation of signaling positive regulation of programmed cell death regulation of apoptotic process biological regulation 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 organonitrogen compound catabolic process catabolic process proteolysis involved in protein catabolic process protein catabolic process macromolecule catabolic process organic substance catabolic process response to organic substance 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 organic substance cellular response to thyroid hormone stimulus cellular response to hormone stimulus biological process involved in interspecies interaction between organisms symbiont entry into host cell viral process symbiont entry into host viral life cycle biological process involved in interaction with host biological process involved in symbiotic interaction fusion of virus membrane with host endosome membrane membrane fusion involved in viral entry into host cell collagen catabolic process collagen metabolic process peptide hormone processing enkephalin processing signaling receptor ligand precursor processing amide metabolic process regulation of biological quality regulation of hormone levels hormone metabolic process import into cell receptor-mediated endocytosis of virus by host cell transport establishment of localization vesicle-mediated transport localization endocytosis involved in viral entry into host cell endocytosis receptor-mediated endocytosis transport of virus 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 membrane organization cellular component organization membrane fusion fusion of virus membrane with host plasma membrane cellular component organization or biogenesis carbohydrate derivative catabolic process glycoprotein catabolic process elastin catabolic process carbohydrate derivative metabolic process glycoprotein metabolic process elastin metabolic process CD4-positive or CD8-positive, alpha-beta T cell lineage commitment multicellular organismal process cellular developmental process cell development mononuclear cell differentiation lymphocyte activation lymphocyte differentiation CD4-positive, alpha-beta T cell differentiation leukocyte activation alpha-beta T cell differentiation T cell activation cell differentiation CD4-positive, alpha-beta T cell activation anatomical structure development alpha-beta T cell activation T cell differentiation CD4-positive, alpha-beta T cell lineage commitment developmental process alpha-beta T cell lineage commitment hemopoiesis cell activation T cell lineage commitment positive T cell selection T cell selection cell fate commitment leukocyte differentiation macrophage apoptotic process myeloid cell apoptotic process leukocyte apoptotic process inflammatory cell apoptotic process zymogen activation	extracellular exosome membrane-bounded organelle extracellular vesicle extracellular organelle extracellular region organelle extracellular space cellular anatomical entity vesicle extracellular membrane-bounded organelle cell periphery extracellular matrix external encapsulating structure collagen-containing extracellular matrix extracellular exosome membrane-bounded organelle extracellular vesicle extracellular organelle extracellular region organelle extracellular space cellular anatomical entity vesicle extracellular membrane-bounded organelle cell periphery extracellular matrix external encapsulating structure collagen-containing extracellular matrix intracellular anatomical structure intracellular vesicle membrane-enclosed lumen lytic vacuole vacuolar lumen endomembrane system intracellular organelle lumen intracellular organelle endolysosome cytoplasmic vesicle endosome lumen lysosome endosome vacuole intracellular membrane-bounded organelle lysosomal lumen organelle lumen endolysosome lumen cytoplasm Golgi apparatus chromaffin granule secretory granule secretory vesicle apical part of cell membrane plasma membrane plasma membrane region apical plasma membrane late endosome multivesicular body endocytic vesicle lumen endocytic vesicle nucleus
B [auth C], D	Cathepsin L	protein binding binding histone binding serpin family protein binding cysteine-type peptidase activity peptidase activity catalytic activity, acting on a protein hydrolase activity catalytic activity enzyme regulator activity enzyme activator activity peptidase regulator activity molecular function activator activity cysteine-type endopeptidase activator activity involved in apoptotic process protein binding binding histone binding serpin family protein binding cysteine-type peptidase activity peptidase activity catalytic activity, acting on a protein hydrolase activity catalytic activity 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 cysteine-type endopeptidase activity endopeptidase activity collagen binding protein-containing complex binding proteoglycan binding carbohydrate derivative binding	organonitrogen compound metabolic process cellular biosynthetic process cellular metabolic process primary metabolic process gene expression macromolecule biosynthetic process protein maturation organic substance metabolic process protein autoprocessing biosynthetic process proteolysis organic substance biosynthetic process protein processing metabolic process organonitrogen compound metabolic process cellular biosynthetic process cellular metabolic process primary metabolic process gene expression macromolecule biosynthetic process protein maturation organic substance metabolic process protein autoprocessing biosynthetic process proteolysis organic substance biosynthetic process protein processing metabolic process cellular process protein metabolic process macromolecule metabolic process response to stimulus immune response immune system process adaptive immune response cellular response to stimulus positive regulation of cell communication regulation of cellular process positive regulation of signal transduction signaling positive regulation of biological process 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 positive regulation of cellular process regulation of biological process regulation of signaling positive regulation of programmed cell death regulation of apoptotic process biological regulation 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 organonitrogen compound catabolic process catabolic process proteolysis involved in protein catabolic process protein catabolic process macromolecule catabolic process organic substance catabolic process response to organic substance 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 organic substance cellular response to thyroid hormone stimulus cellular response to hormone stimulus biological process involved in interspecies interaction between organisms symbiont entry into host cell viral process symbiont entry into host viral life cycle biological process involved in interaction with host biological process involved in symbiotic interaction fusion of virus membrane with host endosome membrane membrane fusion involved in viral entry into host cell collagen catabolic process collagen metabolic process peptide hormone processing enkephalin processing signaling receptor ligand precursor processing amide metabolic process regulation of biological quality regulation of hormone levels hormone metabolic process import into cell receptor-mediated endocytosis of virus by host cell transport establishment of localization vesicle-mediated transport localization endocytosis involved in viral entry into host cell endocytosis receptor-mediated endocytosis transport of virus 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 membrane organization cellular component organization membrane fusion fusion of virus membrane with host plasma membrane cellular component organization or biogenesis carbohydrate derivative catabolic process glycoprotein catabolic process elastin catabolic process carbohydrate derivative metabolic process glycoprotein metabolic process elastin metabolic process CD4-positive or CD8-positive, alpha-beta T cell lineage commitment multicellular organismal process cellular developmental process cell development mononuclear cell differentiation lymphocyte activation lymphocyte differentiation CD4-positive, alpha-beta T cell differentiation leukocyte activation alpha-beta T cell differentiation T cell activation cell differentiation CD4-positive, alpha-beta T cell activation anatomical structure development alpha-beta T cell activation T cell differentiation CD4-positive, alpha-beta T cell lineage commitment developmental process alpha-beta T cell lineage commitment hemopoiesis cell activation T cell lineage commitment positive T cell selection T cell selection cell fate commitment leukocyte differentiation macrophage apoptotic process myeloid cell apoptotic process leukocyte apoptotic process inflammatory cell apoptotic process zymogen activation	extracellular exosome membrane-bounded organelle extracellular vesicle extracellular organelle extracellular region organelle extracellular space cellular anatomical entity vesicle extracellular membrane-bounded organelle cell periphery extracellular matrix external encapsulating structure collagen-containing extracellular matrix extracellular exosome membrane-bounded organelle extracellular vesicle extracellular organelle extracellular region organelle extracellular space cellular anatomical entity vesicle extracellular membrane-bounded organelle cell periphery extracellular matrix external encapsulating structure collagen-containing extracellular matrix intracellular anatomical structure intracellular vesicle membrane-enclosed lumen lytic vacuole vacuolar lumen endomembrane system intracellular organelle lumen intracellular organelle endolysosome cytoplasmic vesicle endosome lumen lysosome endosome vacuole intracellular membrane-bounded organelle lysosomal lumen organelle lumen endolysosome lumen cytoplasm Golgi apparatus chromaffin granule secretory granule secretory vesicle apical part of cell membrane plasma membrane plasma membrane region apical plasma membrane late endosome multivesicular body endocytic vesicle lumen endocytic vesicle nucleus

InterPro: Protein Family Classification InterPro Database Homepage

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

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
A, C [auth B]	Pharos: P07711	meningioma secretory meningioma fibrous meningioma intraorbital meningioma meningothelial meningioma olfactory groove meningioma angiomatous meningioma proteinuria cerebral convexity meningioma spinal meningioma intraventricular meningioma microcystic meningioma parasagittal meningioma benign meningioma psammomatous meningioma meningioma secretory meningioma fibrous meningioma intraorbital meningioma meningothelial meningioma olfactory groove meningioma angiomatous meningioma proteinuria cerebral convexity meningioma spinal meningioma intraventricular meningioma microcystic meningioma parasagittal meningioma benign meningioma psammomatous meningioma clear cell meningioma transitional meningioma large cell medulloblastoma Malignant Meningioma multiple sclerosis pancreatic ductal adenocarcinoma breast cancer psoriasis COVID-19 gastric neoplasm tuberculosis lung carcinoma papillary meningioma cutaneous lupus erythematosus gastric cancer glioblastoma hereditary diffuse gastric adenocarcinoma lymphoplasmacyte-rich meningioma ovarian cancer dermatomyositis gastric carcinoma
B [auth C], D	Pharos: P07711	meningioma secretory meningioma fibrous meningioma intraorbital meningioma meningothelial meningioma olfactory groove meningioma angiomatous meningioma proteinuria cerebral convexity meningioma spinal meningioma intraventricular meningioma microcystic meningioma parasagittal meningioma benign meningioma psammomatous meningioma meningioma secretory meningioma fibrous meningioma intraorbital meningioma meningothelial meningioma olfactory groove meningioma angiomatous meningioma proteinuria cerebral convexity meningioma spinal meningioma intraventricular meningioma microcystic meningioma parasagittal meningioma benign meningioma psammomatous meningioma clear cell meningioma transitional meningioma large cell medulloblastoma Malignant Meningioma multiple sclerosis pancreatic ductal adenocarcinoma breast cancer psoriasis COVID-19 gastric neoplasm tuberculosis lung carcinoma papillary meningioma cutaneous lupus erythematosus gastric cancer glioblastoma hereditary diffuse gastric adenocarcinoma lymphoplasmacyte-rich meningioma ovarian cancer dermatomyositis gastric carcinoma

Protein Modification Annotation

Modified Residue(s)
Chain	Residue(s)	Description
E, F, G, H	BP4
E, F, G, H	DAR
E, F, G, H	PEA
A, C [auth B]	CSD	Parent Component: CYS RESID: AA0262 PSI-MOD : L-cysteine sulfinic acid MOD:00267

RCSB PDB Core Operations are funded by the National Science Foundation (DBI-1832184), 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 R01GM133198.