1VJY | pdb_00001vjy

Crystal Structure of a Naphthyridine Inhibitor of Human TGF-beta Type I Receptor

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	d1vjya_	Alpha and beta proteins (a+b)	Protein kinase-like (PK-like)	Protein kinase-like (PK-like)	Protein kinases, catalytic subunit	Type I TGF-beta receptor R4	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	SCOP2 Family	Protein kinases catalytic domain-like	8028984	4003661	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	Protein kinase-like (PK-like)	8041363	3000066	SCOP2 (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	Pkinase_Tyr	e1vjyA1	A: a+b complex topology	X: Protein kinase/SAICAR synthase/ATP-grasp (From Homology)	H: Protein kinase/SAICAR synthase/ATP-grasp	T: Protein kinase	F: Pkinase_Tyr	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	3.30.200.20	Alpha Beta	2-Layer Sandwich	Phosphorylase Kinase	domain 1	CATH (4.3.0)
A	1.10.510.10	Mainly Alpha	Orthogonal Bundle	Transferase(Phosphotransferase)	domain 1	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A	PF00069	Protein kinase domain (Pkinase)	Protein kinase domain		Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A	TGF-beta receptor type I	protein serine/threonine kinase activity molecular transducer activity catalytic activity, acting on a protein kinase activity protein kinase activity signaling receptor activity transferase activity phosphotransferase activity, alcohol group as acceptor transferase activity, transferring phosphorus-containing groups transmembrane receptor protein serine/threonine kinase activity transforming growth factor beta receptor activity, type II transmembrane receptor protein kinase activity transmembrane signaling receptor activity catalytic activity protein serine/threonine kinase activity molecular transducer activity catalytic activity, acting on a protein kinase activity protein kinase activity signaling receptor activity transferase activity phosphotransferase activity, alcohol group as acceptor transferase activity, transferring phosphorus-containing groups transmembrane receptor protein serine/threonine kinase activity transforming growth factor beta receptor activity, type II transmembrane receptor protein kinase activity transmembrane signaling receptor activity catalytic activity transforming growth factor beta receptor activity binding adenyl ribonucleotide binding nucleotide binding purine ribonucleotide binding purine ribonucleoside triphosphate binding nucleoside phosphate binding ion binding purine nucleotide binding anion binding adenyl nucleotide binding ATP binding heterocyclic compound binding carbohydrate derivative binding ribonucleotide binding small molecule binding transforming growth factor beta receptor activity, type III ubiquitin protein ligase binding protein binding ubiquitin-like protein ligase binding enzyme binding cation binding metal ion binding activin receptor activity activin receptor activity, type II transforming growth factor beta binding growth factor binding cytokine binding SMAD binding transforming growth factor beta receptor activity, type I activin receptor activity, type I protein-containing complex binding activin binding I-SMAD binding transforming growth factor beta receptor binding type II transforming growth factor beta receptor binding signaling receptor binding cytokine receptor binding BMP receptor activity	cellular response to stimulus positive regulation of cell communication cell surface receptor protein serine/threonine kinase signaling pathway regulation of cellular process positive regulation of signal transduction response to stimulus signaling regulation of transmembrane receptor protein serine/threonine kinase signaling pathway positive regulation of biological process regulation of signal transduction intracellular signal transduction cell communication positive regulation of response to stimulus regulation of intracellular signal transduction intracellular signaling cassette cellular response to stimulus positive regulation of cell communication cell surface receptor protein serine/threonine kinase signaling pathway regulation of cellular process positive regulation of signal transduction response to stimulus signaling regulation of transmembrane receptor protein serine/threonine kinase signaling pathway positive regulation of biological process regulation of signal transduction intracellular signal transduction cell communication positive regulation of response to stimulus regulation of intracellular signal transduction intracellular signaling cassette signal transduction enzyme-linked receptor protein signaling pathway positive regulation of cellular process regulation of biological process regulation of signaling cell surface receptor signaling pathway biological regulation positive regulation of intracellular signal transduction positive regulation of transmembrane receptor protein serine/threonine kinase signaling pathway SMAD protein signal transduction regulation of response to stimulus regulation of cell communication cellular process regulation of SMAD protein signal transduction positive regulation of SMAD protein signal transduction positive regulation of signaling developmental process heart development multicellular organism development multicellular organismal process anatomical structure development animal organ development circulatory system development system development cardiac chamber morphogenesis heart morphogenesis ventricular septum development anatomical structure morphogenesis cardiac septum development cardiac septum morphogenesis ventricular septum morphogenesis cardiac chamber development animal organ morphogenesis cardiac ventricle development cellular component organization cellular component organization or biogenesis extracellular structure organization regulation of programmed cell death positive regulation of apoptotic signaling pathway positive regulation of programmed cell death regulation of apoptotic process cell death positive regulation of apoptotic process apoptotic signaling pathway apoptotic process programmed cell death regulation of apoptotic signaling pathway sensory organ development eye development visual system development camera-type eye development sensory system development lens development in camera-type eye endothelial cell migration cell migration cell motility blood vessel morphogenesis tube development artery development vasculature development tube morphogenesis artery morphogenesis blood vessel development angiogenesis involved in coronary vascular morphogenesis coronary vasculature development angiogenesis anatomical structure formation involved in morphogenesis coronary vasculature morphogenesis RNA metabolic process regulation of primary metabolic process nucleobase-containing compound metabolic process RNA biosynthetic process nucleic acid biosynthetic process DNA-templated transcription regulation of RNA metabolic process regulation of nucleobase-containing compound metabolic process regulation of RNA biosynthetic process regulation of biosynthetic process primary metabolic process regulation of macromolecule metabolic process nucleobase-containing compound biosynthetic process gene expression macromolecule biosynthetic process nucleic acid metabolic process regulation of gene expression biosynthetic process metabolic process regulation of macromolecule biosynthetic process regulation of DNA-templated transcription macromolecule metabolic process regulation of metabolic process negative regulation of locomotion regulation of cell motility negative regulation of biological process regulation of locomotion negative regulation of cellular process regulation of cell migration negative regulation of cell motility negative regulation of cell migration locomotion nervous system development skeletal system development skeletal system morphogenesis endocrine system development gland development parathyroid gland development negative regulation of signaling extrinsic apoptotic signaling pathway negative regulation of cell communication negative regulation of extrinsic apoptotic signaling pathway negative regulation of apoptotic signaling pathway negative regulation of response to stimulus negative regulation of programmed cell death negative regulation of signal transduction regulation of extrinsic apoptotic signaling pathway negative regulation of apoptotic process cellular response to growth factor stimulus cellular response to transforming growth factor beta stimulus response to endogenous stimulus cellular response to endogenous stimulus response to transforming growth factor beta transforming growth factor beta receptor signaling pathway response to growth factor transforming growth factor beta receptor superfamily signaling pathway ventricular cardiac muscle tissue morphogenesis striated muscle tissue development muscle structure development ventricular cardiac muscle tissue development ventricular trabecula myocardium morphogenesis muscle tissue development muscle organ development cardiac muscle tissue development tissue development muscle tissue morphogenesis tissue morphogenesis cardiac ventricle morphogenesis cardiac muscle tissue morphogenesis heart trabecula morphogenesis trabecula morphogenesis muscle organ morphogenesis regulation of growth regulation of cellular component organization growth positive regulation of cell growth regulation of cell growth cell growth positive regulation of growth sexual reproduction reproductive process multicellular organismal reproductive process germ cell migration gamete generation regulation of epithelial to mesenchymal transition regulation of developmental process cellular developmental process positive regulation of epithelial to mesenchymal transition regulation of cell differentiation mesenchyme development positive regulation of developmental process positive regulation of cell differentiation cell differentiation regulation of multicellular organismal process epithelial to mesenchymal transition positive regulation of multicellular organismal process mesenchymal cell differentiation positive regulation of cellular component organization positive regulation of cellular component biogenesis positive regulation of extracellular matrix organization extracellular matrix organization regulation of cellular component biogenesis cellular component biogenesis cellular component assembly regulation of extracellular matrix assembly positive regulation of extracellular matrix assembly regulation of extracellular matrix organization extracellular matrix assembly external encapsulating structure organization activin receptor signaling pathway epicardium morphogenesis cell population proliferation positive regulation of cell population proliferation regulation of cell population proliferation positive regulation of cardiac epithelial to mesenchymal transition positive regulation of epithelial to mesenchymal transition involved in endocardial cushion formation endocardial cushion morphogenesis endocardial cushion development cardiac epithelial to mesenchymal transition epithelial to mesenchymal transition involved in endocardial cushion formation regulation of cardiac epithelial to mesenchymal transition mesenchyme morphogenesis endocardial cushion formation regulation of epithelial to mesenchymal transition involved in endocardial cushion formation positive regulation of locomotion positive regulation of cell migration positive regulation of cell motility regulation of protein modification process regulation of post-translational protein modification regulation of protein metabolic process regulation of protein ubiquitination protein ubiquitination macromolecule modification protein metabolic process regulation of protein modification by small protein conjugation or removal protein modification process post-translational protein modification protein modification by small protein conjugation protein modification by small protein conjugation or removal wound healing response to stress response to wounding filopodium assembly cell projection organization regulation of filopodium assembly plasma membrane bounded cell projection assembly positive regulation of cell projection organization positive regulation of filopodium assembly plasma membrane bounded cell projection organization regulation of cell projection organization regulation of cell projection assembly regulation of plasma membrane bounded cell projection assembly cell projection assembly regulation of plasma membrane bounded cell projection organization positive regulation of plasma membrane bounded cell projection assembly myofibroblast differentiation regulation of cartilage development regulation of chondrocyte differentiation connective tissue development negative regulation of cartilage development negative regulation of chondrocyte differentiation negative regulation of cell differentiation regulation of multicellular organismal development negative regulation of developmental process chondrocyte differentiation negative regulation of multicellular organismal process cartilage development endothelial cell proliferation positive regulation of epithelial cell proliferation regulation of endothelial cell proliferation positive regulation of endothelial cell proliferation regulation of epithelial cell proliferation epithelial cell proliferation regulation of cardiac muscle tissue growth developmental growth cardiac muscle cell proliferation organ growth regulation of organ growth regulation of heart growth regulation of cardiac muscle cell proliferation muscle cell proliferation cardiac muscle tissue growth striated muscle cell proliferation heart growth regulation of developmental growth negative regulation of cell population proliferation negative regulation of endothelial cell proliferation negative regulation of epithelial cell proliferation positive regulation of organelle organization regulation of cytoskeleton organization regulation of actin filament-based process regulation of actin filament bundle assembly positive regulation of actin filament bundle assembly actin filament bundle organization positive regulation of stress fiber assembly actin filament-based process stress fiber assembly regulation of actin filament organization actin cytoskeleton organization actomyosin structure organization positive regulation of cytoskeleton organization actin filament organization positive regulation of supramolecular fiber organization regulation of organelle organization regulation of stress fiber assembly organelle organization contractile actin filament bundle assembly regulation of actomyosin structure organization regulation of actin cytoskeleton organization actin filament bundle assembly regulation of supramolecular fiber organization supramolecular fiber organization cytoskeleton organization gonad development reproductive system development sex differentiation developmental process involved in reproduction male gonad development male sex differentiation development of primary male sexual characteristics development of primary sexual characteristics reproductive structure development vascular endothelial cell proliferation positive regulation of macromolecule biosynthetic process positive regulation of metabolic process positive regulation of gene expression positive regulation of biosynthetic process positive regulation of macromolecule metabolic process response to sterol response to lipid response to alcohol response to chemical response to oxygen-containing compound response to cholesterol embryo development ending in birth or egg hatching pharyngeal system development chordate embryonic development embryo development collagen fibril organization in utero embryonic development mesenchymal stem cell proliferation regulation of stem cell proliferation positive regulation of mesenchymal stem cell proliferation regulation of mesenchymal stem cell proliferation positive regulation of stem cell proliferation stem cell proliferation cellular component disassembly regulation of tight junction disassembly cell junction disassembly tight junction organization positive regulation of tight junction disassembly tight junction disassembly cell junction organization cell-cell junction disassembly cell-cell junction organization protein phosphorylation phosphorylation peptidyl-serine modification peptidyl-serine phosphorylation peptidyl-amino acid modification phosphate-containing compound metabolic process phosphorus metabolic process kidney development renal system development immune system development hematopoietic or lymphoid organ development thymus development immune system process embryonic organ morphogenesis embryonic cranial skeleton morphogenesis embryonic morphogenesis cranial skeletal system development embryonic skeletal system development embryonic organ development embryonic skeletal system morphogenesis regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction phosphatidylinositol 3-kinase/protein kinase B signal transduction neuron fate commitment generation of neurons neurogenesis neuron differentiation cell fate commitment coronary artery morphogenesis regulation of vasculature development positive regulation of vasculature development positive regulation of DNA-templated transcription positive regulation of nucleobase-containing compound metabolic process positive regulation of RNA metabolic process positive regulation of RNA biosynthetic process cell cycle regulation of cell cycle ventricular compact myocardium morphogenesis blastocyst development post-embryonic development anterior/posterior pattern specification pattern specification process regionalization roof of mouth development endothelial cell activation cell activation	protein-containing complex receptor complex cell surface cellular anatomical structure cell periphery plasma membrane membrane membrane microdomain membrane raft membrane-bounded organelle intracellular anatomical structure endosome intracellular vesicle intracellular membrane-bounded organelle protein-containing complex receptor complex cell surface cellular anatomical structure cell periphery plasma membrane membrane membrane microdomain membrane raft membrane-bounded organelle intracellular anatomical structure endosome intracellular vesicle intracellular membrane-bounded organelle endomembrane system intracellular organelle cytoplasmic vesicle organelle cytoplasm vesicle catalytic complex plasma membrane protein complex membrane protein complex transferase complex protein kinase complex transferase complex, transferring phosphorus-containing groups serine/threonine protein kinase complex transforming growth factor beta ligand-receptor complex plasma membrane signaling receptor complex activin receptor complex cell-cell junction apical junction complex bicellular tight junction tight junction anchoring junction cell junction nucleus

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A	IPR000472	Activin types I and II receptor domain	Domain
A	IPR000719	Protein kinase domain	Domain
A	IPR003605	GS domain	Domain
A	IPR017441	Protein kinase, ATP binding site	Binding Site
A	IPR008271	Serine/threonine-protein kinase, active site	Active Site
A	IPR000333	Ser/Thr protein kinase, TGFB receptor	Family
A	IPR045860	Snake toxin-like superfamily	Homologous Superfamily
A	IPR011009	Protein kinase-like domain superfamily	Homologous Superfamily

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
A	Pharos: P36897	Loeys-Dietz syndrome thoracic aortic aneurysm craniosynostosis Aneurysm, Dissecting multiple self-healing squamous epithelioma skin cancer Loeys-Dietz syndrome 1 skin neoplasm cirrhosis of liver uremia colorectal cancer pilocytic astrocytoma familial thoracic aortic aneurysm and aortic dissection Gaucher disease wet macular degeneration Loeys-Dietz syndrome thoracic aortic aneurysm craniosynostosis Aneurysm, Dissecting multiple self-healing squamous epithelioma skin cancer Loeys-Dietz syndrome 1 skin neoplasm cirrhosis of liver uremia colorectal cancer pilocytic astrocytoma familial thoracic aortic aneurysm and aortic dissection Gaucher disease wet macular degeneration allergic rhinitis large cell medulloblastoma arthrogryposis cancer malignant glioma medulloblastoma colorectal carcinoma myopathy ovarian cancer primitive neuroectodermal tumor drug-induced liver injury ulcerative colitis glioblastoma intellectual disability astrocytic tumor cerebrovascular disorder malignant pancreatic neoplasm oligodendroglioma Crohn disease pancreatic intraductal papillary-mucinous neoplasm with low grade dysplasia prostate cancer Ehlers-Danlos syndrome age-related macular degeneration juvenile dermatomyositis aortic aneurysm breast cancer malignant ependymoma Marfan syndrome osteosarcoma

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.