5U7R | pdb_00005u7r

Identification of A New Class of Potent Cdc7 Inhibitors Designed by Putative Pharmacophore Model: Synthesis and Biological Evaluation of 2,3-Dihydrothieno[3,2-d]pyrimidin-4(1H)-ones

External Resource: Annotation

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: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
D	SCOP2B Superfamily	Protein kinase-like (PK-like)	8098222	3000066	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	Protein kinase-like (PK-like)	8098222	3000066	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Protein kinase-like (PK-like)	8098222	3000066	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	Protein kinase-like (PK-like)	8098222	3000066	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	Sigma70_r4_2	e5u7rD1	A: alpha bundles	X: Spectrin repeat-like	H: TIM barrels	T: TIM barrels	F: Sigma70_r4_2	ECOD (develop294)
C	Sigma70_r4_2	e5u7rC1	A: alpha bundles	X: Spectrin repeat-like	H: TIM barrels	T: TIM barrels	F: Sigma70_r4_2	ECOD (develop294)
B	Sigma70_r4_2	e5u7rB1	A: alpha bundles	X: Spectrin repeat-like	H: TIM barrels	T: TIM barrels	F: Sigma70_r4_2	ECOD (develop294)
A	Sigma70_r4_2	e5u7rA1	A: alpha bundles	X: Spectrin repeat-like	H: TIM barrels	T: TIM barrels	F: Sigma70_r4_2	ECOD (develop294)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
D	3.30.200.20	Alpha Beta	2-Layer Sandwich	Phosphorylase Kinase	domain 1	CATH (4.3.0)
D	1.10.510.10	Mainly Alpha	Orthogonal Bundle	Transferase(Phosphotransferase)	domain 1	CATH (4.3.0)
C	3.30.200.20	Alpha Beta	2-Layer Sandwich	Phosphorylase Kinase	domain 1	CATH (4.3.0)
C	1.10.510.10	Mainly Alpha	Orthogonal Bundle	Transferase(Phosphotransferase)	domain 1	CATH (4.3.0)
B	3.30.200.20	Alpha Beta	2-Layer Sandwich	Phosphorylase Kinase	domain 1	CATH (4.3.0)
B	1.10.510.10	Mainly Alpha	Orthogonal Bundle	Transferase(Phosphotransferase)	domain 1	CATH (4.3.0)
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, B, C, D	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, B, C, D	Rho-associated protein kinase 2	small GTPase binding protein binding binding enzyme binding GTPase binding protein serine/threonine kinase activity tau-protein kinase activity catalytic activity, acting on a protein kinase activity protein kinase activity transferase activity catalytic activity phosphotransferase activity, alcohol group as acceptor transferase activity, transferring phosphorus-containing groups small GTPase binding protein binding binding enzyme binding GTPase binding protein serine/threonine kinase activity tau-protein kinase activity catalytic activity, acting on a protein kinase activity protein kinase activity transferase activity catalytic activity phosphotransferase activity, alcohol group as acceptor transferase activity, transferring phosphorus-containing groups 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 cytoskeletal protein binding tau protein binding Rho-dependent protein serine/threonine kinase activity protease binding RNA binding nucleic acid binding protein serine kinase activity structural molecule activity cation binding transition metal ion binding zinc ion binding metal ion binding endopeptidase activator activity enzyme regulator activity enzyme activator activity peptidase regulator activity molecular function activator activity molecular function regulator activity peptidase activator activity endopeptidase regulator activity	regulation of cellular process regulation of cellular component organization cell-substrate junction assembly cellular component organization cellular component biogenesis cell adhesion cellular component assembly cell junction assembly regulation of cell-substrate junction organization cellular component organization or biogenesis focal adhesion assembly regulation of biological process regulation of cell-substrate adhesion regulation of cell adhesion regulation of cellular process regulation of cellular component organization cell-substrate junction assembly cellular component organization cellular component biogenesis cell adhesion cellular component assembly cell junction assembly regulation of cell-substrate junction organization cellular component organization or biogenesis focal adhesion assembly regulation of biological process regulation of cell-substrate adhesion regulation of cell adhesion biological regulation cell-substrate adhesion regulation of cellular component biogenesis regulation of cell junction assembly cell junction organization cell-matrix adhesion regulation of cell-matrix adhesion cell-substrate junction organization cellular process regulation of focal adhesion assembly regulation of cell-substrate junction assembly amyloid precursor protein catabolic process positive regulation of protein metabolic process regulation of protein metabolic process positive regulation of biological process primary metabolic process regulation of amyloid precursor protein catabolic process regulation of macromolecule metabolic process regulation of primary metabolic process positive regulation of metabolic process metabolic process positive regulation of macromolecule metabolic process protein metabolic process macromolecule metabolic process positive regulation of amyloid precursor protein catabolic process amyloid precursor protein metabolic process regulation of metabolic process positive regulation of cellular process positive regulation of centrosome duplication microtubule cytoskeleton organization centrosome duplication centrosome cycle positive regulation of cell cycle process cell cycle regulation of cell cycle cell cycle process microtubule organizing center organization regulation of centrosome cycle regulation of cell cycle process regulation of microtubule-based process positive regulation of cell cycle organelle organization regulation of centrosome duplication microtubule-based process cytoskeleton organization regulation of biosynthetic process gene expression macromolecule biosynthetic process positive regulation of macromolecule biosynthetic process regulation of gene expression biosynthetic process positive regulation of gene expression positive regulation of biosynthetic process regulation of macromolecule biosynthetic process response to stimulus response to stress response to ischemia response to angiotensin response to hormone response to chemical response to endogenous stimulus response to peptide hormone response to oxygen-containing compound response to nitrogen compound localization protein localization to cell periphery cellular localization protein localization to plasma membrane macromolecule localization intracellular protein localization localization within membrane protein localization to membrane multicellular organismal process regulation of connective tissue growth factor production cytokine production regulation of cytokine production regulation of multicellular organismal process connective tissue growth factor production positive regulation of multicellular organismal process positive regulation of cytokine production positive regulation of connective tissue growth factor production actin cytoskeleton organization actin filament-based process developmental process multicellular organism development anatomical structure morphogenesis embryonic morphogenesis anatomical structure development embryo development cellular response to stimulus response to decreased oxygen levels regulation of cellular response to hypoxia cellular response to oxygen levels cellular response to hypoxia regulation of cellular response to stress cellular response to decreased oxygen levels cellular response to chemical stimulus cellular response to stress regulation of response to stimulus response to hypoxia regulation of response to stress response to oxygen levels response to abiotic stimulus cortical actin cytoskeleton organization cortical cytoskeleton organization cellular developmental process cell differentiation animal organ development mesenchyme development mesenchymal cell differentiation tissue development epithelial to mesenchymal transition protein phosphorylation phosphorylation macromolecule modification phosphate-containing compound metabolic process protein modification process phosphorus metabolic process biological process involved in interspecies interaction between organisms host-mediated perturbation of viral process modulation of process of another organism host-mediated perturbation of symbiont process muscle hypertrophy regulation of muscle adaptation system process positive regulation of cardiac muscle hypertrophy regulation of system process striated muscle hypertrophy regulation of muscle system process muscle system process regulation of cardiac muscle hypertrophy regulation of muscle hypertrophy muscle adaptation positive regulation of muscle hypertrophy cardiac muscle hypertrophy cellular response to nitrogen compound cellular response to acetylcholine cellular response to oxygen-containing compound response to acetylcholine negative regulation of biological process nucleobase-containing compound metabolic process post-transcriptional regulation of gene expression regulation of RNA metabolic process regulation of nucleobase-containing compound metabolic process regulation of biological quality RNA catabolic process mRNA catabolic process negative regulation of metabolic process positive regulation of mRNA metabolic process nucleobase-containing compound catabolic process positive regulation of RNA metabolic process negative regulation of gene expression negative regulation of macromolecule biosynthetic process nucleic acid catabolic process catabolic process RNA metabolic process mRNA destabilization macromolecule catabolic process regulation of mRNA catabolic process negative regulation of cellular process negative regulation of macromolecule metabolic process RNA destabilization regulation of catabolic process mRNA metabolic process nucleic acid metabolic process positive regulation of catabolic process regulation of mRNA stability negative regulation of biosynthetic process positive regulation of mRNA catabolic process regulation of RNA stability regulation of mRNA metabolic process small GTPase-mediated signal transduction signaling Rho protein signal transduction intracellular signal transduction cell communication intracellular signaling cassette signal transduction regulation of fibroblast growth factor production positive regulation of fibroblast growth factor production fibroblast growth factor production nervous system process regulation of nervous system process mitotic cell cycle process cytoskeleton-dependent cytokinesis mitotic cytokinesis cytokinesis cell division mitotic cell cycle regulation of cytoskeleton organization regulation of actin filament-based process regulation of actin filament bundle assembly actin filament bundle organization stress fiber assembly regulation of actin filament organization actomyosin structure organization actin filament organization regulation of organelle organization regulation of stress fiber assembly 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 rhythmic process circadian rhythm regulation of circadian rhythm response to transforming growth factor beta response to growth factor smooth muscle contraction muscle contraction positive regulation of tissue remodeling positive regulation of connective tissue replacement regulation of tissue remodeling tissue remodeling connective tissue replacement regulation of connective tissue replacement bicellular tight junction assembly tight junction organization negative regulation of cell junction assembly cell-cell junction assembly cell-cell junction organization regulation of bicellular tight junction assembly negative regulation of cellular component organization apical junction assembly tight junction assembly negative regulation of bicellular tight junction assembly regulation of nitric oxide biosynthetic process reactive nitrogen species metabolic process nitric oxide metabolic process nitric oxide biosynthetic process negative regulation of nitric oxide biosynthetic process regulation of nitric oxide metabolic process regulation of localization positive regulation of protein localization to early endosome regulation of protein localization protein localization to endosome protein localization to early endosome regulation of protein localization to endosome protein localization to organelle positive regulation of protein localization positive regulation of protein localization to endosome regulation of protein localization to early endosome regulation of developmental process regulation of epidermal cell differentiation epidermis development regulation of cell differentiation epithelial cell differentiation regulation of epithelial cell differentiation epithelium development regulation of multicellular organismal development epidermal cell differentiation skin development keratinocyte differentiation regulation of epidermis development regulation of keratinocyte differentiation heart development heart valve development aortic valve development circulatory system development heart valve morphogenesis semi-lunar valve development aortic valve morphogenesis system development regulation of amyloid-beta formation positive regulation of amyloid-beta formation amyloid-beta metabolic process amyloid-beta formation positive regulation of cell communication positive regulation of signal transduction regulation of signal transduction positive regulation of response to stimulus regulation of intracellular signal transduction regulation of signaling positive regulation of MAPK cascade positive regulation of intracellular signal transduction regulation of MAPK cascade MAPK cascade regulation of cell communication positive regulation of signaling negative regulation of protein localization to lysosome protein localization to vacuole regulation of protein localization to lysosome protein localization to lysosome negative regulation of protein localization angiotensin-activated signaling pathway cellular response to angiotensin cellular response to endogenous stimulus regulation of G protein-coupled receptor signaling pathway cellular response to hormone stimulus cellular response to peptide hormone stimulus regulation of angiotensin-activated signaling pathway G protein-coupled receptor signaling pathway positive regulation of locomotion regulation of cell motility positive regulation of cell migration regulation of locomotion positive regulation of cell motility regulation of cell migration cell migration cell motility locomotion regulation of establishment of endothelial barrier endothelium development cell development regulation of cell development endothelial cell development regulation of endothelial cell development endothelial cell differentiation regulation of endothelial cell differentiation epithelial cell development establishment of endothelial barrier negative regulation of developmental process negative regulation of biomineral tissue development regulation of biomineral tissue development biomineral tissue development angiogenesis regulation of vasculature development tube morphogenesis regulation of anatomical structure morphogenesis blood vessel development blood vessel morphogenesis tube development negative regulation of blood vessel morphogenesis negative regulation of angiogenesis vasculature development negative regulation of vasculature development regulation of angiogenesis anatomical structure formation involved in morphogenesis negative regulation of multicellular organismal process regulation of tube diameter regulation of tube size circulatory system process vascular process in circulatory system blood vessel diameter maintenance blood circulation regulation of anatomical structure size positive regulation of organelle organization positive regulation of cellular component organization positive regulation of actin filament bundle assembly positive regulation of stress fiber assembly positive regulation of cellular component biogenesis positive regulation of cytoskeleton organization positive regulation of supramolecular fiber organization regulation of establishment of cell polarity regulation of establishment or maintenance of cell polarity establishment of cell polarity establishment or maintenance of cell polarity	cellular anatomical structure intracellular anatomical structure cytoplasm cytosol intracellular organelle cytoskeleton organelle membraneless organelle intracellular membraneless organelle centrosome microtubule organizing center microtubule cytoskeleton cell periphery plasma membrane cellular anatomical structure intracellular anatomical structure cytoplasm cytosol intracellular organelle cytoskeleton organelle membraneless organelle intracellular membraneless organelle centrosome microtubule organizing center microtubule cytoskeleton cell periphery plasma membrane membrane cytoplasmic ribonucleoprotein granule supramolecular complex ribonucleoprotein granule membrane-bounded organelle nucleus intracellular membrane-bounded organelle

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B, C, D	IPR000719	Protein kinase domain	Domain
A, B, C, D	IPR037311	Rho-associated protein kinase 2, HR1 domain	Domain
A, B, C, D	IPR057529	MRCK/ROCK kinase, PH domain	Domain
A, B, C, D	IPR011072	HR1 rho-binding domain	Domain
A, B, C, D	IPR017441	Protein kinase, ATP binding site	Binding Site
A, B, C, D	IPR001849	Pleckstrin homology domain	Domain
A, B, C, D	IPR050839	Rho-associated Serine/Threonine Kinase	Family
A, B, C, D	IPR011993	PH-like domain superfamily	Homologous Superfamily
A, B, C, D	IPR000961	AGC-kinase, C-terminal	Domain
A, B, C, D	IPR029878	Rho-associated protein kinase 2, catalytic domain	Domain
A, B, C, D	IPR002219	Protein kinase C-like, phorbol ester/diacylglycerol-binding domain	Domain
A, B, C, D	IPR011009	Protein kinase-like domain superfamily	Homologous Superfamily
A, B, C, D	IPR020684	Rho-associated protein kinase 1/2	Family
A, B, C, D	IPR015008	ROCK, Rho binding domain	Domain
A, B, C, D	IPR046349	C1-like domain superfamily	Homologous Superfamily
A, B, C, D	IPR008271	Serine/threonine-protein kinase, active site	Active Site

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
A, B, C, D	Pharos: O75116	Prenatal Injuries astrocytic tumor hereditary spastic paraplegia malignant ependymoma ocular hypertension osteosarcoma skin basal cell carcinoma atypical teratoid rhabdoid tumor esophageal adenocarcinoma large cell medulloblastoma medulloblastoma oligodendroglioma ovarian cancer glaucoma lung cancer Prenatal Injuries astrocytic tumor hereditary spastic paraplegia malignant ependymoma ocular hypertension osteosarcoma skin basal cell carcinoma atypical teratoid rhabdoid tumor esophageal adenocarcinoma large cell medulloblastoma medulloblastoma oligodendroglioma ovarian cancer glaucoma lung cancer metastatic melanoma open-angle glaucoma

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.