1MHW | pdb_00001mhw

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: ECOD 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)
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)
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)
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)

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
D		e1mhwD01	A: alpha bundles	X: RNase A-like	H: RNase A-like	T: RNase A-like	F:	ECOD (develop294)
B [auth C]		e1mhwC01	A: alpha bundles	X: RNase A-like	H: RNase A-like	T: RNase A-like	F:	ECOD (develop294)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
D	2.40.50.170	Mainly Beta	Beta Barrel	OB fold (Dihydrolipoamide Acetyltransferase, E2P)	Cysteine proteinases. Chain C	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)
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)

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

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	-	-	-
B [auth C], D	Cathepsin L	protein binding binding histone binding cysteine-type peptidase activity peptidase activity catalytic activity, acting on a protein cysteine-type endopeptidase activity hydrolase activity catalytic activity endopeptidase activity serpin family protein binding collagen binding protein-containing complex binding fibronectin binding protein binding binding histone binding cysteine-type peptidase activity peptidase activity catalytic activity, acting on a protein cysteine-type endopeptidase activity hydrolase activity catalytic activity endopeptidase activity serpin family protein binding collagen binding protein-containing complex binding fibronectin binding proteoglycan binding carbohydrate derivative binding	viral process fusion of virus membrane with host endosome membrane membrane fusion involved in viral entry into host cell collagen catabolic process catabolic process metabolic process cellular process collagen metabolic process primary metabolic process gene expression macromolecule biosynthetic process protein maturation protein autoprocessing biosynthetic process viral process fusion of virus membrane with host endosome membrane membrane fusion involved in viral entry into host cell collagen catabolic process catabolic process metabolic process cellular process collagen metabolic process primary metabolic process gene expression macromolecule biosynthetic process protein maturation protein autoprocessing biosynthetic process proteolysis protein processing protein metabolic process macromolecule metabolic process response to stimulus immune response immune system process adaptive immune response peptide hormone processing regulation of hormone levels enkephalin processing biological regulation signaling receptor ligand precursor processing hormone metabolic process regulation of biological quality import into cell receptor-mediated endocytosis of virus by host cell biological process involved in interspecies interaction between organisms transport viral life cycle establishment of localization biological process involved in interaction with host vesicle-mediated transport biological process involved in symbiotic interaction localization symbiont entry into host cell symbiont entry into host endocytosis involved in viral entry into host cell receptor-mediated endocytosis endocytosis 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 protein catabolic process glycoprotein metabolic process macromolecule catabolic 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 cellular response to stimulus 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 macrophage apoptotic process myeloid cell apoptotic process leukocyte apoptotic process inflammatory cell apoptotic process apoptotic process cell death programmed cell death zymogen activation	cell periphery cellular anatomical structure apical part of cell membrane plasma membrane plasma membrane region apical plasma membrane membrane-bounded organelle intracellular anatomical structure membrane-enclosed lumen lytic vacuole vacuolar lumen vacuole intracellular membrane-bounded organelle cell periphery cellular anatomical structure apical part of cell membrane plasma membrane plasma membrane region apical plasma membrane membrane-bounded organelle intracellular anatomical structure membrane-enclosed lumen lytic vacuole vacuolar lumen vacuole intracellular membrane-bounded organelle lysosomal lumen intracellular organelle lumen intracellular organelle organelle lumen organelle cytoplasm lysosome extracellular exosome extracellular vesicle extracellular organelle extracellular region extracellular space vesicle extracellular membrane-bounded organelle intracellular vesicle endomembrane system endolysosome cytoplasmic vesicle endosome lumen endosome endolysosome lumen extracellular matrix external encapsulating structure late endosome multivesicular body Golgi apparatus endocytic vesicle lumen endocytic vesicle nucleus chromaffin granule secretory granule secretory vesicle
A, C [auth B]	Cathepsin L	protein binding binding histone binding cysteine-type peptidase activity peptidase activity catalytic activity, acting on a protein cysteine-type endopeptidase activity hydrolase activity catalytic activity endopeptidase activity serpin family protein binding collagen binding protein-containing complex binding fibronectin binding protein binding binding histone binding cysteine-type peptidase activity peptidase activity catalytic activity, acting on a protein cysteine-type endopeptidase activity hydrolase activity catalytic activity endopeptidase activity serpin family protein binding collagen binding protein-containing complex binding fibronectin binding proteoglycan binding carbohydrate derivative binding	viral process fusion of virus membrane with host endosome membrane membrane fusion involved in viral entry into host cell collagen catabolic process catabolic process metabolic process cellular process collagen metabolic process primary metabolic process gene expression macromolecule biosynthetic process protein maturation protein autoprocessing biosynthetic process viral process fusion of virus membrane with host endosome membrane membrane fusion involved in viral entry into host cell collagen catabolic process catabolic process metabolic process cellular process collagen metabolic process primary metabolic process gene expression macromolecule biosynthetic process protein maturation protein autoprocessing biosynthetic process proteolysis protein processing protein metabolic process macromolecule metabolic process response to stimulus immune response immune system process adaptive immune response peptide hormone processing regulation of hormone levels enkephalin processing biological regulation signaling receptor ligand precursor processing hormone metabolic process regulation of biological quality import into cell receptor-mediated endocytosis of virus by host cell biological process involved in interspecies interaction between organisms transport viral life cycle establishment of localization biological process involved in interaction with host vesicle-mediated transport biological process involved in symbiotic interaction localization symbiont entry into host cell symbiont entry into host endocytosis involved in viral entry into host cell receptor-mediated endocytosis endocytosis 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 protein catabolic process glycoprotein metabolic process macromolecule catabolic 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 cellular response to stimulus 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 macrophage apoptotic process myeloid cell apoptotic process leukocyte apoptotic process inflammatory cell apoptotic process apoptotic process cell death programmed cell death zymogen activation	cell periphery cellular anatomical structure apical part of cell membrane plasma membrane plasma membrane region apical plasma membrane membrane-bounded organelle intracellular anatomical structure membrane-enclosed lumen lytic vacuole vacuolar lumen vacuole intracellular membrane-bounded organelle cell periphery cellular anatomical structure apical part of cell membrane plasma membrane plasma membrane region apical plasma membrane membrane-bounded organelle intracellular anatomical structure membrane-enclosed lumen lytic vacuole vacuolar lumen vacuole intracellular membrane-bounded organelle lysosomal lumen intracellular organelle lumen intracellular organelle organelle lumen organelle cytoplasm lysosome extracellular exosome extracellular vesicle extracellular organelle extracellular region extracellular space vesicle extracellular membrane-bounded organelle intracellular vesicle endomembrane system endolysosome cytoplasmic vesicle endosome lumen endosome endolysosome lumen extracellular matrix external encapsulating structure late endosome multivesicular body Golgi apparatus endocytic vesicle lumen endocytic vesicle nucleus chromaffin granule secretory granule secretory vesicle

InterPro: Protein Family Classification InterPro Database Homepage

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

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
B [auth C], D	Pharos: P07711	meningioma secretory meningioma fibrous meningioma intraorbital meningioma meningothelial meningioma olfactory groove meningioma angiomatous meningioma cerebral convexity meningioma proteinuria spinal meningioma intraventricular meningioma microcystic meningioma benign meningioma parasagittal meningioma clear cell meningioma meningioma secretory meningioma fibrous meningioma intraorbital meningioma meningothelial meningioma olfactory groove meningioma angiomatous meningioma cerebral convexity meningioma proteinuria spinal meningioma intraventricular meningioma microcystic meningioma benign meningioma parasagittal meningioma clear cell meningioma psammomatous meningioma transitional meningioma large cell medulloblastoma Malignant Meningioma multiple sclerosis pancreatic ductal adenocarcinoma breast cancer COVID-19 psoriasis tuberculosis gastric neoplasm lung carcinoma papillary meningioma cutaneous lupus erythematosus gastric cancer glioblastoma hereditary diffuse gastric adenocarcinoma lymphoplasmacyte-rich meningioma ovarian cancer dermatomyositis gastric carcinoma
A, C [auth B]	Pharos: P07711	meningioma secretory meningioma fibrous meningioma intraorbital meningioma meningothelial meningioma olfactory groove meningioma angiomatous meningioma cerebral convexity meningioma proteinuria spinal meningioma intraventricular meningioma microcystic meningioma benign meningioma parasagittal meningioma clear cell meningioma meningioma secretory meningioma fibrous meningioma intraorbital meningioma meningothelial meningioma olfactory groove meningioma angiomatous meningioma cerebral convexity meningioma proteinuria spinal meningioma intraventricular meningioma microcystic meningioma benign meningioma parasagittal meningioma clear cell meningioma psammomatous meningioma transitional meningioma large cell medulloblastoma Malignant Meningioma multiple sclerosis pancreatic ductal adenocarcinoma breast cancer COVID-19 psoriasis tuberculosis gastric neoplasm 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 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. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.