9H5N | pdb_00009h5n

Crystal structure of Thrombin in complex with a Chlorothiophene-based inhibitor, CP3, discovered by a novel rapid nanoscale library screening.

External Resource: Annotation

Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification
Pharos: Disease Associations

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
D	SCOP2B Superfamily	Trypsin-like serine proteases	8042154	3000114	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Trypsin-like serine proteases	8042154	3000114	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)
D	PAD_N	e9h5nD1	A: alpha arrays	X: Hypothetical protein YqbG-like	H: Hypothetical protein YqbG-like	T: alpha/beta-Hydrolases	F: PAD_N	ECOD (v295.2)
B	Cry1Ac_D5	e9h5nB1	A: alpha arrays	X: Hypothetical protein YqbG-like	H: Hypothetical protein YqbG-like	T: alpha/beta-Hydrolases	F: Cry1Ac_D5	ECOD (v295.2)
C	PAD_N	e9h5nC1	A: alpha arrays	X: Hypothetical protein YqbG-like	H: Hypothetical protein YqbG-like	T: alpha/beta-Hydrolases	F: PAD_N	ECOD (v295.2)
A	Cry1Ac_D5	e9h5nA1	A: alpha arrays	X: Hypothetical protein YqbG-like	H: Hypothetical protein YqbG-like	T: alpha/beta-Hydrolases	F: Cry1Ac_D5	ECOD (v295.2)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
B, D	PF00089	Trypsin (Trypsin)	Trypsin		Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
B, D	Prothrombin	molecular function activator activity molecular function regulator activity signaling receptor regulator activity growth factor activity receptor ligand activity signaling receptor activator activity peptidase activity catalytic activity, acting on a protein serine hydrolase activity serine-type peptidase activity hydrolase activity serine-type endopeptidase activity catalytic activity endopeptidase activity molecular function activator activity molecular function regulator activity signaling receptor regulator activity growth factor activity receptor ligand activity signaling receptor activator activity peptidase activity catalytic activity, acting on a protein serine hydrolase activity serine-type peptidase activity hydrolase activity serine-type endopeptidase activity catalytic activity endopeptidase activity cation binding ion binding binding calcium ion binding metal ion binding small molecule binding protein binding signaling receptor binding lipid binding lipopolysaccharide binding carbohydrate derivative binding molecular transducer activity signaling receptor activity thrombospondin receptor activity heparin binding glycosaminoglycan binding sulfur compound binding	multicellular organismal process regulation of body fluid levels wound healing response to stimulus hemostasis biological regulation blood coagulation response to stress coagulation regulation of biological quality response to wounding neutrophil-mediated killing of symbiont cell biological process involved in interspecies interaction between organisms disruption of cell in another organism multicellular organismal process regulation of body fluid levels wound healing response to stimulus hemostasis biological regulation blood coagulation response to stress coagulation regulation of biological quality response to wounding neutrophil-mediated killing of symbiont cell biological process involved in interspecies interaction between organisms disruption of cell in another organism defense response to Gram-negative bacterium response to biotic stimulus myeloid leukocyte mediated immunity defense response to bacterium neutrophil mediated immunity response to bacterium leukocyte mediated immunity response to external biotic stimulus killing of cells of another organism neutrophil-mediated killing of bacterium neutrophil mediated cytotoxicity response to other organism defense response response to external stimulus leukocyte mediated cytotoxicity immune effector process neutrophil-mediated killing of gram-negative bacterium immune system process cellular process disruption of anatomical structure in another organism cell killing cellular response to stimulus regulation of biological process regulation of cellular process signaling cell communication thrombin-activated receptor signaling pathway G protein-coupled receptor signaling pathway signal transduction regulation of response to external stimulus negative regulation of biological process regulation of response to wounding regulation of coagulation regulation of response to stress regulation of multicellular organismal process regulation of hemostasis negative regulation of response to stimulus negative regulation of wound healing regulation of blood coagulation negative regulation of blood coagulation negative regulation of response to wounding negative regulation of hemostasis fibrinolysis negative regulation of coagulation regulation of response to stimulus negative regulation of response to external stimulus regulation of wound healing negative regulation of multicellular organismal process inorganic ion homeostasis intracellular calcium ion homeostasis homeostatic process calcium ion homeostasis regulation of cytosolic calcium ion concentration cellular homeostasis chemical homeostasis intracellular monoatomic cation homeostasis monoatomic ion homeostasis intracellular chemical homeostasis monoatomic cation homeostasis intracellular monoatomic ion homeostasis cell activation platelet activation positive regulation of coagulation positive regulation of biological process positive regulation of blood coagulation positive regulation of response to stimulus positive regulation of hemostasis positive regulation of response to wounding positive regulation of wound healing positive regulation of multicellular organismal process regulation of biosynthetic process collagen biosynthetic process regulation of collagen biosynthetic process regulation of collagen metabolic process positive regulation of metabolic process positive regulation of collagen metabolic process biosynthetic process positive regulation of biosynthetic process positive regulation of collagen biosynthetic process metabolic process collagen metabolic process regulation of metabolic process positive regulation of cellular process regulation of cell activation negative regulation of platelet activation negative regulation of cellular process negative regulation of cell activation regulation of platelet activation cellular developmental process regulation of developmental process astrocyte differentiation cell development regulation of neurogenesis regulation of cell differentiation regulation of gliogenesis regulation of astrocyte differentiation regulation of cell development regulation of nervous system development multicellular organism development neurogenesis negative regulation of neurogenesis gliogenesis cell differentiation anatomical structure development negative regulation of nervous system development negative regulation of cell differentiation system development developmental process regulation of multicellular organismal development negative regulation of developmental process regulation of glial cell differentiation nervous system development negative regulation of astrocyte differentiation negative regulation of gliogenesis negative regulation of cell development negative regulation of glial cell differentiation central nervous system development glial cell differentiation animal gross anatomical part developmental process regulation of localization regulation of protein localization positive regulation of protein localization to nucleus regulation of protein localization to nucleus protein localization to nucleus localization macromolecule localization protein localization to organelle positive regulation of protein localization intracellular protein localization negative regulation of proteolysis regulation of protein metabolic process negative regulation of metabolic process primary metabolic process regulation of macromolecule metabolic process regulation of primary metabolic process regulation of proteolysis proteolysis protein metabolic process macromolecule metabolic process negative regulation of protein metabolic process negative regulation of macromolecule metabolic process reactive oxygen species metabolic process positive regulation of reactive oxygen species metabolic process regulation of reactive oxygen species metabolic process positive regulation of cell communication positive regulation of signal transduction regulation of signal transduction phospholipase C-activating G protein-coupled receptor signaling pathway regulation of G protein-coupled receptor signaling pathway regulation of signaling positive regulation of G protein-coupled receptor signaling pathway positive regulation of phospholipase C-activating G protein-coupled receptor signaling pathway regulation of cell communication regulation of phospholipase C-activating G protein-coupled receptor signaling pathway positive regulation of signaling positive regulation of response to external stimulus regulation of fibrinolysis negative regulation of fibrinolysis cell surface receptor signaling pathway humoral immune response immune response defense response to symbiont antimicrobial humoral response antimicrobial humoral immune response mediated by antimicrobial peptide defense response to other organism cell surface receptor signaling pathway via STAT positive regulation of receptor signaling pathway via STAT positive regulation of receptor signaling pathway via JAK-STAT regulation of receptor signaling pathway via JAK-STAT regulation of receptor signaling pathway via STAT cell surface receptor signaling pathway via JAK-STAT regulation of calcium ion transport positive regulation of cation transmembrane transport positive regulation of calcium ion transport transport monoatomic ion transmembrane transport regulation of monoatomic ion transmembrane transport calcium ion transport metal ion transport regulation of calcium ion transmembrane transport monoatomic cation transmembrane transport positive regulation of monoatomic ion transport positive regulation of calcium ion transmembrane transport positive regulation of transmembrane transport monoatomic ion transport positive regulation of monoatomic ion transmembrane transport positive regulation of release of sequestered calcium ion into cytosol monoatomic cation transport regulation of metal ion transport calcium ion transmembrane import into cytosol regulation of transport regulation of release of sequestered calcium ion into cytosol regulation of monoatomic ion transport establishment of localization transmembrane transport release of sequestered calcium ion into cytosol regulation of transmembrane transport positive regulation of transport regulation of monoatomic cation transmembrane transport calcium ion transmembrane transport regulation of cytokine production involved in inflammatory response cytokine production regulation of cytokine production negative regulation of cytokine production involved in inflammatory response production of molecular mediator involved in inflammatory response negative regulation of cytokine production cytokine production involved in inflammatory response gene expression macromolecule biosynthetic process regulation of gene expression negative regulation of gene expression negative regulation of biosynthetic process negative regulation of macromolecule biosynthetic process regulation of macromolecule biosynthetic process inflammatory response	extracellular exosome membrane-bounded organelle extracellular vesicle cellular anatomical structure extracellular organelle extracellular region organelle vesicle extracellular membrane-bounded organelle intracellular anatomical structure membrane-enclosed lumen intracellular membrane-bounded organelle endomembrane system intracellular organelle lumen extracellular exosome membrane-bounded organelle extracellular vesicle cellular anatomical structure extracellular organelle extracellular region organelle vesicle extracellular membrane-bounded organelle intracellular anatomical structure membrane-enclosed lumen intracellular membrane-bounded organelle endomembrane system intracellular organelle lumen endoplasmic reticulum lumen intracellular organelle organelle lumen endoplasmic reticulum cytoplasm cell periphery plasma membrane membrane extracellular matrix external encapsulating structure Golgi apparatus Golgi lumen blood microparticle
A, C	Thrombin light chain	molecular function activator activity molecular function regulator activity signaling receptor regulator activity growth factor activity receptor ligand activity signaling receptor activator activity peptidase activity catalytic activity, acting on a protein serine hydrolase activity serine-type peptidase activity hydrolase activity serine-type endopeptidase activity catalytic activity endopeptidase activity molecular function activator activity molecular function regulator activity signaling receptor regulator activity growth factor activity receptor ligand activity signaling receptor activator activity peptidase activity catalytic activity, acting on a protein serine hydrolase activity serine-type peptidase activity hydrolase activity serine-type endopeptidase activity catalytic activity endopeptidase activity cation binding ion binding binding calcium ion binding metal ion binding small molecule binding protein binding signaling receptor binding lipid binding lipopolysaccharide binding carbohydrate derivative binding molecular transducer activity signaling receptor activity thrombospondin receptor activity heparin binding glycosaminoglycan binding sulfur compound binding	multicellular organismal process regulation of body fluid levels wound healing response to stimulus hemostasis biological regulation blood coagulation response to stress coagulation regulation of biological quality response to wounding neutrophil-mediated killing of symbiont cell biological process involved in interspecies interaction between organisms disruption of cell in another organism multicellular organismal process regulation of body fluid levels wound healing response to stimulus hemostasis biological regulation blood coagulation response to stress coagulation regulation of biological quality response to wounding neutrophil-mediated killing of symbiont cell biological process involved in interspecies interaction between organisms disruption of cell in another organism defense response to Gram-negative bacterium response to biotic stimulus myeloid leukocyte mediated immunity defense response to bacterium neutrophil mediated immunity response to bacterium leukocyte mediated immunity response to external biotic stimulus killing of cells of another organism neutrophil-mediated killing of bacterium neutrophil mediated cytotoxicity response to other organism defense response response to external stimulus leukocyte mediated cytotoxicity immune effector process neutrophil-mediated killing of gram-negative bacterium immune system process cellular process disruption of anatomical structure in another organism cell killing cellular response to stimulus regulation of biological process regulation of cellular process signaling cell communication thrombin-activated receptor signaling pathway G protein-coupled receptor signaling pathway signal transduction regulation of response to external stimulus negative regulation of biological process regulation of response to wounding regulation of coagulation regulation of response to stress regulation of multicellular organismal process regulation of hemostasis negative regulation of response to stimulus negative regulation of wound healing regulation of blood coagulation negative regulation of blood coagulation negative regulation of response to wounding negative regulation of hemostasis fibrinolysis negative regulation of coagulation regulation of response to stimulus negative regulation of response to external stimulus regulation of wound healing negative regulation of multicellular organismal process inorganic ion homeostasis intracellular calcium ion homeostasis homeostatic process calcium ion homeostasis regulation of cytosolic calcium ion concentration cellular homeostasis chemical homeostasis intracellular monoatomic cation homeostasis monoatomic ion homeostasis intracellular chemical homeostasis monoatomic cation homeostasis intracellular monoatomic ion homeostasis cell activation platelet activation positive regulation of coagulation positive regulation of biological process positive regulation of blood coagulation positive regulation of response to stimulus positive regulation of hemostasis positive regulation of response to wounding positive regulation of wound healing positive regulation of multicellular organismal process regulation of biosynthetic process collagen biosynthetic process regulation of collagen biosynthetic process regulation of collagen metabolic process positive regulation of metabolic process positive regulation of collagen metabolic process biosynthetic process positive regulation of biosynthetic process positive regulation of collagen biosynthetic process metabolic process collagen metabolic process regulation of metabolic process positive regulation of cellular process regulation of cell activation negative regulation of platelet activation negative regulation of cellular process negative regulation of cell activation regulation of platelet activation cellular developmental process regulation of developmental process astrocyte differentiation cell development regulation of neurogenesis regulation of cell differentiation regulation of gliogenesis regulation of astrocyte differentiation regulation of cell development regulation of nervous system development multicellular organism development neurogenesis negative regulation of neurogenesis gliogenesis cell differentiation anatomical structure development negative regulation of nervous system development negative regulation of cell differentiation system development developmental process regulation of multicellular organismal development negative regulation of developmental process regulation of glial cell differentiation nervous system development negative regulation of astrocyte differentiation negative regulation of gliogenesis negative regulation of cell development negative regulation of glial cell differentiation central nervous system development glial cell differentiation animal gross anatomical part developmental process regulation of localization regulation of protein localization positive regulation of protein localization to nucleus regulation of protein localization to nucleus protein localization to nucleus localization macromolecule localization protein localization to organelle positive regulation of protein localization intracellular protein localization negative regulation of proteolysis regulation of protein metabolic process negative regulation of metabolic process primary metabolic process regulation of macromolecule metabolic process regulation of primary metabolic process regulation of proteolysis proteolysis protein metabolic process macromolecule metabolic process negative regulation of protein metabolic process negative regulation of macromolecule metabolic process reactive oxygen species metabolic process positive regulation of reactive oxygen species metabolic process regulation of reactive oxygen species metabolic process positive regulation of cell communication positive regulation of signal transduction regulation of signal transduction phospholipase C-activating G protein-coupled receptor signaling pathway regulation of G protein-coupled receptor signaling pathway regulation of signaling positive regulation of G protein-coupled receptor signaling pathway positive regulation of phospholipase C-activating G protein-coupled receptor signaling pathway regulation of cell communication regulation of phospholipase C-activating G protein-coupled receptor signaling pathway positive regulation of signaling positive regulation of response to external stimulus regulation of fibrinolysis negative regulation of fibrinolysis cell surface receptor signaling pathway humoral immune response immune response defense response to symbiont antimicrobial humoral response antimicrobial humoral immune response mediated by antimicrobial peptide defense response to other organism cell surface receptor signaling pathway via STAT positive regulation of receptor signaling pathway via STAT positive regulation of receptor signaling pathway via JAK-STAT regulation of receptor signaling pathway via JAK-STAT regulation of receptor signaling pathway via STAT cell surface receptor signaling pathway via JAK-STAT regulation of calcium ion transport positive regulation of cation transmembrane transport positive regulation of calcium ion transport transport monoatomic ion transmembrane transport regulation of monoatomic ion transmembrane transport calcium ion transport metal ion transport regulation of calcium ion transmembrane transport monoatomic cation transmembrane transport positive regulation of monoatomic ion transport positive regulation of calcium ion transmembrane transport positive regulation of transmembrane transport monoatomic ion transport positive regulation of monoatomic ion transmembrane transport positive regulation of release of sequestered calcium ion into cytosol monoatomic cation transport regulation of metal ion transport calcium ion transmembrane import into cytosol regulation of transport regulation of release of sequestered calcium ion into cytosol regulation of monoatomic ion transport establishment of localization transmembrane transport release of sequestered calcium ion into cytosol regulation of transmembrane transport positive regulation of transport regulation of monoatomic cation transmembrane transport calcium ion transmembrane transport regulation of cytokine production involved in inflammatory response cytokine production regulation of cytokine production negative regulation of cytokine production involved in inflammatory response production of molecular mediator involved in inflammatory response negative regulation of cytokine production cytokine production involved in inflammatory response gene expression macromolecule biosynthetic process regulation of gene expression negative regulation of gene expression negative regulation of biosynthetic process negative regulation of macromolecule biosynthetic process regulation of macromolecule biosynthetic process inflammatory response	extracellular exosome membrane-bounded organelle extracellular vesicle cellular anatomical structure extracellular organelle extracellular region organelle vesicle extracellular membrane-bounded organelle intracellular anatomical structure membrane-enclosed lumen intracellular membrane-bounded organelle endomembrane system intracellular organelle lumen extracellular exosome membrane-bounded organelle extracellular vesicle cellular anatomical structure extracellular organelle extracellular region organelle vesicle extracellular membrane-bounded organelle intracellular anatomical structure membrane-enclosed lumen intracellular membrane-bounded organelle endomembrane system intracellular organelle lumen endoplasmic reticulum lumen intracellular organelle organelle lumen endoplasmic reticulum cytoplasm cell periphery plasma membrane membrane extracellular matrix external encapsulating structure Golgi apparatus Golgi lumen blood microparticle

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
B, D	IPR018992	Thrombin light chain	Domain
B, D	IPR037111	Thrombin light chain domain superfamily	Homologous Superfamily
B, D	IPR003966	Prothrombin/thrombin	Family
B, D	IPR009003	Peptidase S1, PA clan	Homologous Superfamily
B, D	IPR033116	Serine proteases, trypsin family, serine active site	Active Site
B, D	IPR001254	Serine proteases, trypsin domain	Domain
B, D	IPR035972	Gamma-carboxyglutamic acid-rich (GLA) domain superfamily	Homologous Superfamily
B, D	IPR000001	Kringle	Domain
B, D	IPR000294	Gamma-carboxyglutamic acid-rich (GLA) domain	Domain
B, D	IPR051659	Serine Protease S1 Domain-Containing Protein	Family
B, D	IPR018056	Kringle, conserved site	Conserved Site
B, D	IPR018114	Serine protease-like, trypsin family, histidine active site	Active Site
B, D	IPR013806	Kringle-like fold	Homologous Superfamily
B, D	IPR038178	Kringle superfamily	Homologous Superfamily
B, D	IPR001314	Peptidase S1A, chymotrypsin family	Family
A, C	IPR018992	Thrombin light chain	Domain
A, C	IPR037111	Thrombin light chain domain superfamily	Homologous Superfamily
A, C	IPR003966	Prothrombin/thrombin	Family
A, C	IPR009003	Peptidase S1, PA clan	Homologous Superfamily
A, C	IPR033116	Serine proteases, trypsin family, serine active site	Active Site
A, C	IPR001254	Serine proteases, trypsin domain	Domain
A, C	IPR035972	Gamma-carboxyglutamic acid-rich (GLA) domain superfamily	Homologous Superfamily
A, C	IPR000001	Kringle	Domain
A, C	IPR000294	Gamma-carboxyglutamic acid-rich (GLA) domain	Domain
A, C	IPR051659	Serine Protease S1 Domain-Containing Protein	Family
A, C	IPR018056	Kringle, conserved site	Conserved Site
A, C	IPR018114	Serine protease-like, trypsin family, histidine active site	Active Site
A, C	IPR013806	Kringle-like fold	Homologous Superfamily
A, C	IPR038178	Kringle superfamily	Homologous Superfamily
A, C	IPR001314	Peptidase S1A, chymotrypsin family	Family

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
B, D	: P00734	congenital prothrombin deficiency thrombophilia pregnancy loss, recurrent, susceptibility to, 2 liver failure cirrhosis of liver Venous Thrombosis intracranial sinus thrombosis brain ischemia myocardial infarction disseminated intravascular coagulation Alzheimer disease rheumatoid arthritis thrombotic disease hepatocellular carcinoma schizophrenia congenital prothrombin deficiency thrombophilia pregnancy loss, recurrent, susceptibility to, 2 liver failure cirrhosis of liver Venous Thrombosis intracranial sinus thrombosis brain ischemia myocardial infarction disseminated intravascular coagulation Alzheimer disease rheumatoid arthritis thrombotic disease hepatocellular carcinoma schizophrenia non-alcoholic fatty liver disease obesity disorder paratuberculosis skin vascular disease thrombophilia due to thrombin defect cerebrovascular disorder nephrosis venous thromboembolism cerebral infarction COVID-19 varicose disease osteoarthritis anemia pulmonary embolism autoimmune disease esophageal varices vascular disease vitamin K deficiency hemorrhagic disease heart disease alcohol abuse hepatic encephalopathy inborn carbohydrate metabolic disorder respiratory failure blood coagulation disease cancer liver disease thrombocytopenia coronary artery disease fatty liver disease hemochromatosis type 1 pneumonia hepatitis B virus infection hypertensive disorder autism spectrum disorder kidney disease
A, C	: P00734	congenital prothrombin deficiency thrombophilia pregnancy loss, recurrent, susceptibility to, 2 liver failure cirrhosis of liver Venous Thrombosis intracranial sinus thrombosis brain ischemia myocardial infarction disseminated intravascular coagulation Alzheimer disease rheumatoid arthritis thrombotic disease hepatocellular carcinoma schizophrenia congenital prothrombin deficiency thrombophilia pregnancy loss, recurrent, susceptibility to, 2 liver failure cirrhosis of liver Venous Thrombosis intracranial sinus thrombosis brain ischemia myocardial infarction disseminated intravascular coagulation Alzheimer disease rheumatoid arthritis thrombotic disease hepatocellular carcinoma schizophrenia non-alcoholic fatty liver disease obesity disorder paratuberculosis skin vascular disease thrombophilia due to thrombin defect cerebrovascular disorder nephrosis venous thromboembolism cerebral infarction COVID-19 varicose disease osteoarthritis anemia pulmonary embolism autoimmune disease esophageal varices vascular disease vitamin K deficiency hemorrhagic disease heart disease alcohol abuse hepatic encephalopathy inborn carbohydrate metabolic disorder respiratory failure blood coagulation disease cancer liver disease thrombocytopenia coronary artery disease fatty liver disease hemochromatosis type 1 pneumonia hepatitis B virus infection hypertensive disorder autism spectrum disorder kidney disease