3DEK | pdb_00003dek

Crystal Structures of Caspase-3 with Bound Isoquinoline-1,3,4-trione Derivative Inhibitors

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
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	d3deka_	Alpha and beta proteins (a/b)	Caspase-like	Caspase-like	Caspase catalytic domain	automated matches	Human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
C	d3dekc_	Alpha and beta proteins (a/b)	Caspase-like	Caspase-like	Caspase catalytic domain	automated matches	Human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
D	d3dekd_	Alpha and beta proteins (a/b)	Caspase-like	Caspase-like	Caspase catalytic domain	automated matches	Human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
B	d3dekb_	Alpha and beta proteins (a/b)	Caspase-like	Caspase-like	Caspase catalytic domain	automated matches	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	Caspase-like	8033452	3001096	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	Caspase-like	8033452	3001096	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	Caspase-like	8033452	3001096	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Caspase-like	8033452	3001096	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_C14	e3dekA1	A: a/b three-layered sandwiches	X: Caspase-like (From Topology)	H: Caspase-like (From Topology)	T: Caspase-like	F: Peptidase_C14	ECOD (1.6)
C	Peptidase_C14	e3dekC1	A: a/b three-layered sandwiches	X: Caspase-like (From Topology)	H: Caspase-like (From Topology)	T: Caspase-like	F: Peptidase_C14	ECOD (1.6)
D	Peptidase_C14	e3dekD1	A: a/b three-layered sandwiches	X: Caspase-like (From Topology)	H: Caspase-like (From Topology)	T: Caspase-like	F: Peptidase_C14	ECOD (1.6)
B	Peptidase_C14	e3dekB1	A: a/b three-layered sandwiches	X: Caspase-like (From Topology)	H: Caspase-like (From Topology)	T: Caspase-like	F: Peptidase_C14	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	3.40.50.1460	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold		CATH (4.3.0)
C	3.40.50.1460	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold		CATH (4.3.0)
D	3.40.50.1460	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold		CATH (4.3.0)
B	3.40.50.1460	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold		CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B, C, D	PF00656	Caspase domain (Peptidase_C14)	Caspase domain		Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B, C, D	Caspase-3	enzyme regulator activity cyclin-dependent protein kinase regulator activity enzyme inhibitor activity protein kinase regulator activity protein kinase inhibitor activity molecular function inhibitor activity cyclin-dependent protein serine/threonine kinase inhibitor activity molecular function regulator activity cyclin-dependent protein serine/threonine kinase regulator activity protein serine/threonine kinase inhibitor activity kinase inhibitor activity kinase regulator activity protein-containing complex binding binding enzyme regulator activity cyclin-dependent protein kinase regulator activity enzyme inhibitor activity protein kinase regulator activity protein kinase inhibitor activity molecular function inhibitor activity cyclin-dependent protein serine/threonine kinase inhibitor activity molecular function regulator activity cyclin-dependent protein serine/threonine kinase regulator activity protein serine/threonine kinase inhibitor activity kinase inhibitor activity kinase regulator activity protein-containing complex binding binding protein binding signaling receptor binding cytokine receptor binding tumor necrosis factor receptor superfamily binding death receptor binding peptidase activity catalytic activity, acting on a protein hydrolase activity catalytic activity cysteine-type peptidase activity cysteine-type endopeptidase activity endopeptidase activity enzyme binding protease binding aspartic-type peptidase activity aspartic-type endopeptidase activity enzyme activator activity molecular function activator activity phospholipase A2 activator activity phospholipase activator activity lipase activator activity	cellular response to stimulus cellular response to stress response to stimulus DNA damage response response to stress cellular process response to chemical response to xenobiotic stimulus developmental process heart development multicellular organism development multicellular organismal process anatomical structure development animal organ development cellular response to stimulus cellular response to stress response to stimulus DNA damage response response to stress cellular process response to chemical response to xenobiotic stimulus developmental process heart development multicellular organism development multicellular organismal process anatomical structure development animal organ development circulatory system development system development negative regulation of lymphocyte proliferation regulation of cellular process regulation of leukocyte activation negative regulation of biological process regulation of cell activation lymphocyte activation negative regulation of lymphocyte activation leukocyte proliferation leukocyte activation negative regulation of mononuclear cell proliferation negative regulation of leukocyte proliferation regulation of B cell proliferation lymphocyte proliferation regulation of B cell activation negative regulation of cellular process regulation of immune system process regulation of multicellular organismal process negative regulation of B cell activation regulation of lymphocyte proliferation regulation of leukocyte proliferation regulation of biological process negative regulation of cell population proliferation cell population proliferation B cell activation biological regulation cell activation B cell proliferation negative regulation of B cell proliferation negative regulation of cell activation negative regulation of immune system process regulation of cell population proliferation mononuclear cell proliferation immune system process regulation of mononuclear cell proliferation negative regulation of multicellular organismal process negative regulation of leukocyte activation regulation of lymphocyte activation leukocyte apoptotic process apoptotic process cell death programmed cell death catabolic process macroautophagy autophagy regulation of catabolic process regulation of autophagy regulation of macroautophagy metabolic process process utilizing autophagic mechanism regulation of metabolic process glial cell apoptotic process response to X-ray response to ionizing radiation response to radiation response to abiotic stimulus negative regulation of cell cycle cell cycle regulation of cell cycle primary metabolic process protein catabolic process protein metabolic process macromolecule metabolic process macromolecule catabolic process neuron apoptotic process positive regulation of programmed cell death regulation of apoptotic process positive regulation of biological process regulation of programmed cell death positive regulation of apoptotic process positive regulation of neuron apoptotic process positive regulation of cellular process regulation of neuron apoptotic process signaling cellular response to chemical stress intracellular signal transduction cellular response to environmental stimulus cell communication signal transduction intrinsic apoptotic signaling pathway response to osmotic stress cellular response to osmotic stress apoptotic signaling pathway cellular response to chemical stimulus intrinsic apoptotic signaling pathway in response to osmotic stress cellular response to abiotic stimulus B cell homeostasis multicellular organismal-level homeostasis leukocyte homeostasis homeostatic process homeostasis of number of cells lymphocyte homeostasis response to anesthetic fibroblast apoptotic process cytokine production regulation of cytokine production negative regulation of macromolecule metabolic process regulation of biosynthetic process negative regulation of metabolic process negative regulation of cytokine production regulation of macromolecule metabolic process gene expression macromolecule biosynthetic process regulation of gene expression negative regulation of gene expression biosynthetic process negative regulation of biosynthetic process negative regulation of macromolecule biosynthetic process regulation of macromolecule biosynthetic process regulation of protein stability regulation of biological quality response to light stimulus response to UV response to wounding cellular developmental process cell differentiation cell fate commitment system process sensory perception nervous system process sensory perception of sound sensory perception of mechanical stimulus response to decreased oxygen levels response to hypoxia response to oxygen levels hemopoiesis cell development erythrocyte differentiation myeloid cell differentiation myeloid cell homeostasis erythrocyte homeostasis neuron recognition cell projection organization neuron projection development neuron projection fasciculation cellular component organization neurogenesis neuron differentiation axonal fasciculation cell recognition cellular component organization or biogenesis plasma membrane bounded cell projection organization nervous system development axon development generation of neurons neuron development muscle structure development striated muscle cell differentiation muscle cell differentiation response to hydrogen peroxide response to oxidative stress response to oxygen-containing compound response to reactive oxygen species regulation of localization cellular localization transport regulation of transport regulation of synaptic vesicle cycle synaptic vesicle cycle regulation of vesicle-mediated transport establishment of localization vesicle-mediated transport vesicle-mediated transport in synapse localization establishment of localization in cell response to acid chemical response to amino acid epithelium development epidermal cell differentiation epidermis development tissue development epithelial cell differentiation skin development keratinocyte differentiation head development forebrain development brain development pallium development central nervous system development telencephalon development hippocampus development limbic system development negative regulation of T cell proliferation negative regulation of cell adhesion T cell activation negative regulation of T cell activation negative regulation of leukocyte cell-cell adhesion negative regulation of cell-cell adhesion regulation of leukocyte cell-cell adhesion regulation of activated T cell proliferation leukocyte cell-cell adhesion activated T cell proliferation cell adhesion cell-cell adhesion regulation of cell-cell adhesion T cell proliferation regulation of cell adhesion regulation of T cell activation regulation of T cell proliferation negative regulation of activated T cell proliferation epithelial cell apoptotic process T cell homeostasis execution phase of apoptosis protein maturation proteolysis protein processing response to hexose response to monosaccharide response to carbohydrate response to glucose embryonic epithelial tube formation chordate embryonic development anterior neural tube closure tube formation embryo development epithelial tube formation tube morphogenesis primary neural tube formation embryo development ending in birth or egg hatching epithelial tube morphogenesis morphogenesis of embryonic epithelium neural tube development tube development embryonic morphogenesis morphogenesis of an epithelium anatomical structure morphogenesis tissue morphogenesis neural tube closure neural tube formation anatomical structure formation involved in morphogenesis tube closure response to corticosteroid response to lipid response to hormone response to steroid hormone response to endogenous stimulus response to glucocorticoid cellular response to nitrogen compound cellular response to staurosporine response to staurosporine response to nitrogen compound response to alkaloid cellular response to alkaloid regulation of amide metabolic process amyloid precursor protein catabolic process positive regulation of protein metabolic process regulation of amyloid-beta formation positive regulation of amyloid-beta formation regulation of amyloid precursor protein catabolic process regulation of primary metabolic process positive regulation of metabolic process amyloid-beta metabolic process positive regulation of macromolecule metabolic process amide metabolic process amyloid precursor protein metabolic process amyloid-beta formation regulation of protein metabolic process positive regulation of amide metabolic process positive regulation of amyloid precursor protein catabolic process platelet morphogenesis cell morphogenesis platelet formation rhythmic process ovulation cycle process gonad development reproductive system development reproductive process female gonad development sex differentiation multicellular organismal reproductive process female sex differentiation development of primary female sexual characteristics developmental process involved in reproduction ovulation cycle development of primary sexual characteristics reproductive structure development luteolysis regulation of defense response regulation of response to external stimulus defense response pyroptotic inflammatory response response to external stimulus regulation of inflammatory response positive regulation of response to stimulus positive regulation of response to external stimulus positive regulation of inflammatory response regulation of response to stimulus regulation of response to stress positive regulation of defense response positive regulation of pyroptotic inflammatory response inflammatory response behavior learning or memory cognition cellular response to growth factor stimulus cell surface receptor signaling pathway neurotrophin TRK receptor signaling pathway cell surface receptor protein tyrosine kinase signaling pathway cellular response to endogenous stimulus neurotrophin signaling pathway response to growth factor enzyme-linked receptor protein signaling pathway response to nicotine response to cobalt ion response to metal ion biological process involved in interspecies interaction between organisms response to other organism response to lipopolysaccharide response to biotic stimulus response to bacterium response to external biotic stimulus response to molecule of bacterial origin response to estradiol response to peptide response to cytokine response to tumor necrosis factor	cellular anatomical structure intracellular anatomical structure cytoplasm cytosol synapse cell junction glutamatergic synapse somatodendritic compartment cell body neuronal cell body cell periphery protein-containing complex plasma membrane protein complex membrane cellular anatomical structure intracellular anatomical structure cytoplasm cytosol synapse cell junction glutamatergic synapse somatodendritic compartment cell body neuronal cell body cell periphery protein-containing complex plasma membrane protein complex membrane plasma membrane death-inducing signaling complex membrane protein complex membrane-bounded organelle nucleus membrane-enclosed lumen intracellular membrane-bounded organelle intracellular organelle lumen intracellular organelle nucleoplasm organelle lumen organelle nuclear lumen postsynaptic density postsynapse neuron to neuron synapse postsynaptic specialization asymmetric synapse

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B, C, D	IPR029030	Caspase-like domain superfamily	Homologous Superfamily
A, B, C, D	IPR001309	Peptidase C14, p20 domain	Domain
A, B, C, D	IPR011600	Peptidase C14, caspase domain	Domain
A, B, C, D	IPR016129	Peptidase family C14A, His active site	Active Site
A, B, C, D	IPR015917	Peptidase C14A, caspase catalytic domain	Domain
A, B, C, D	IPR033139	Peptidase family C14A, cysteine active site	Active Site
A, B, C, D	IPR002138	Peptidase C14, caspase non-catalytic subunit p10	Domain
A, B, C, D	IPR002398	Peptidase C14 family	Family

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
A, B, C, D	Pharos: P42574	Alzheimer disease status epilepticus diabetic retinopathy ulcerative colitis Diabetes Mellitus, Experimental diabetic polyneuropathy heart valve disease retinal detachment diabetic autonomic neuropathy diabetic neuropathy type 2 diabetes mellitus calcinosis cryptorchidism diabetic peripheral angiopathy myocardial infarction Alzheimer disease status epilepticus diabetic retinopathy ulcerative colitis Diabetes Mellitus, Experimental diabetic polyneuropathy heart valve disease retinal detachment diabetic autonomic neuropathy diabetic neuropathy type 2 diabetes mellitus calcinosis cryptorchidism diabetic peripheral angiopathy myocardial infarction subarachnoid hemorrhage nervous system disorder toxic encephalopathy brain ischemia colonic disease coronary artery disease ischemia reperfusion injury schizophrenia lung cancer maturity-onset diabetes of the young mucocutaneous lymph node syndrome stomach disease neurodegenerative disease eye disease ovarian cancer autoimmune disease glioblastoma pancreatic intraductal papillary-mucinous neoplasm breast disease prostate disease intracerebral hemorrhage kidney disease lung disease spinal cord injury ovarian disease pancreatic intraductal papillary-mucinous neoplasm with low grade dysplasia uterine disease hematologic disease inborn carbohydrate metabolic disorder invasive ductal breast carcinoma liver disease lymphatic system disease pancreatic intraductal papillary-mucinous carcinoma heart disease cancer vertebral column disease hepatitis cerebrovascular disorder

Protein Modification Annotation

Modified Residue(s)
Chain	Residue(s)	Description
A, B, C, D	OCS	Parent Component: CYS RESID: AA0556 PSI-MOD : L-cysteic acid (L-cysteine sulfonic acid) MOD:00460

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.