3NDM | pdb_00003ndm

Crystal structure of Rho-Associated Protein Kinase (ROCK1) with a potent isoquinolone derivative

External Resource: Annotation

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

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
D	FAD_binding_4	e3ndmD1	A: alpha bundles	X: Lipocalins/Streptavidin	H: Zn-dependent exopeptidases	T: Zn-dependent exopeptidases	F: FAD_binding_4	ECOD (develop294)
C	FAD_binding_4	e3ndmC1	A: alpha bundles	X: Lipocalins/Streptavidin	H: Zn-dependent exopeptidases	T: Zn-dependent exopeptidases	F: FAD_binding_4	ECOD (develop294)
B	FAD_binding_4	e3ndmB1	A: alpha bundles	X: Lipocalins/Streptavidin	H: Zn-dependent exopeptidases	T: Zn-dependent exopeptidases	F: FAD_binding_4	ECOD (develop294)
A	SIR2	e3ndmA2	A: alpha bundles	X: Rossmann-like	H: Glycosyl hydrolase domain	T: Glycosyl hydrolase domain	F: SIR2	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 (ROCK1)	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 protein serine kinase activity cation binding transition metal ion binding zinc ion binding metal ion binding	leukocyte tethering or rolling leukocyte cell-cell adhesion leukocyte migration cell adhesion cell-cell adhesion immune system process leukocyte adhesion to vascular endothelial cell cellular extravasation cell migration cellular process cell motility regulation of cellular process regulation of cellular component organization cell-substrate junction assembly leukocyte tethering or rolling leukocyte cell-cell adhesion leukocyte migration cell adhesion cell-cell adhesion immune system process leukocyte adhesion to vascular endothelial cell cellular extravasation cell migration cellular process cell motility regulation of cellular process regulation of cellular component organization cell-substrate junction assembly cellular component organization cellular component biogenesis 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 regulation of focal adhesion assembly regulation of cell-substrate junction assembly regulation of protein binding regulation of molecular function negative regulation of protein binding regulation of binding negative regulation of binding negative regulation of molecular function muscle cell migration myoblast migration membrane to membrane docking membrane docking regulation of biosynthetic process positive regulation of biological process regulation of macromolecule metabolic process gene expression macromolecule biosynthetic process positive regulation of macromolecule biosynthetic process regulation of gene expression positive regulation of metabolic process biosynthetic process positive regulation of gene expression positive regulation of biosynthetic process regulation of macromolecule biosynthetic process metabolic process positive regulation of macromolecule metabolic process macromolecule metabolic process regulation of metabolic process positive regulation of cellular process response to angiotensin response to stimulus 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 organelle organization actin cytoskeleton organization actin filament-based process cytoskeleton organization regulation of localization import into cell transport synaptic vesicle cycle regulation of synaptic vesicle recycling vesicle-mediated transport presynaptic endocytosis vesicle-mediated transport in synapse synaptic vesicle recycling regulation of synaptic vesicle endocytosis establishment of localization in cell regulation of endocytosis synaptic vesicle endocytosis regulation of transport regulation of vesicle-mediated transport establishment of localization endocytosis positive regulation of cellular component organization positive regulation of cell-substrate junction organization positive regulation of cell-substrate adhesion positive regulation of focal adhesion assembly positive regulation of cellular component biogenesis positive regulation of cell adhesion positive regulation of cell-matrix adhesion positive regulation of cell junction assembly regulation of cell motility regulation of locomotion regulation of cell migration locomotion developmental process multicellular organism development multicellular organismal process anatomical structure morphogenesis embryonic morphogenesis anatomical structure development embryo development regulation of developmental process nervous system development developmental maturation synapse maturation regulation of synapse organization regulation of synapse maturation regulation of synapse structure or activity synapse organization regulation of biological quality system development 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 amyloid precursor protein catabolic process regulation of amyloid-beta formation negative regulation of biological process regulation of amyloid precursor protein catabolic process regulation of primary metabolic process negative regulation of amyloid precursor protein catabolic process amyloid-beta metabolic process negative regulation of cellular process protein metabolic process amyloid precursor protein metabolic process negative regulation of protein metabolic process amyloid-beta formation negative regulation of macromolecule metabolic process negative regulation of amyloid-beta formation regulation of protein metabolic process negative regulation of metabolic process primary metabolic 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 regulation of response to stimulus positive regulation of muscle hypertrophy cardiac muscle hypertrophy positive regulation of multicellular organismal process regulation of multicellular organismal process protein phosphorylation phosphorylation peptidyl-serine modification peptidyl-serine phosphorylation macromolecule modification peptidyl-amino acid modification phosphate-containing compound metabolic process protein modification process phosphorus metabolic process nucleobase-containing compound metabolic process post-transcriptional regulation of gene expression regulation of RNA metabolic process regulation of nucleobase-containing compound metabolic process RNA catabolic process mRNA catabolic 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 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 cellular response to stimulus small GTPase-mediated signal transduction signaling Rho protein signal transduction intracellular signal transduction cell communication intracellular signaling cassette signal transduction positive regulation of autophagy autophagy regulation of autophagy process utilizing autophagic mechanism plasma membrane bounded cell projection organization cell projection organization cell development neuron projection development generation of neurons neurogenesis neuron differentiation neuron development mitotic cell cycle process cytoskeleton-dependent cytokinesis mitotic cytokinesis cytokinesis cell division cell cycle mitotic cell cycle cell cycle process epithelium migration tissue migration ameboidal-type cell migration podocyte cell migration epithelial cell migration 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 bleb assembly plasma membrane bounded cell projection assembly cell projection assembly neuron apoptotic process apoptotic process motor neuron apoptotic process cell death programmed cell death response to transforming growth factor beta response to growth factor smooth muscle contraction muscle contraction positive regulation of amyloid-beta clearance amyloid-beta clearance regulation of amyloid-beta clearance epithelium development actin filament-based movement cell morphogenesis epithelial cell differentiation epithelial cell development epithelial cell morphogenesis actin-mediated cell contraction apical constriction 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 microtubule cytoskeleton organization regulation of microtubule-based process microtubule-based process regulation of microtubule cytoskeleton organization regulation of epidermal cell differentiation epidermis development regulation of cell differentiation regulation of epithelial cell differentiation 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 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 cellular response to nitrogen compound 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 cellular response to oxygen-containing compound regulation of angiotensin-activated signaling pathway cellular response to chemical stimulus G protein-coupled receptor signaling pathway regulation of neuron differentiation regulation of establishment of endothelial barrier endothelium development regulation of cell development endothelial cell development regulation of endothelial cell development endothelial cell differentiation regulation of endothelial cell differentiation establishment of endothelial barrier negative regulation of developmental process negative regulation of biomineral tissue development regulation of biomineral tissue development biomineral tissue development negative regulation of membrane protein ectodomain proteolysis negative regulation of proteolysis negative regulation of protein catabolic process regulation of proteolysis proteolysis membrane protein proteolysis membrane protein ectodomain proteolysis negative regulation of catabolic process regulation of membrane protein ectodomain proteolysis protein catabolic process regulation of protein catabolic process 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 plasma membrane bounded cell projection morphogenesis cell projection morphogenesis neuron projection morphogenesis neuron projection arborization 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 negative regulation of neuron apoptotic process negative regulation of programmed cell death regulation of apoptotic process regulation of programmed cell death regulation of motor neuron apoptotic process negative regulation of apoptotic process negative regulation of motor neuron apoptotic process regulation of neuron apoptotic process regulation of establishment of cell polarity regulation of establishment or maintenance of cell polarity establishment of cell polarity establishment or maintenance of cell polarity	cell projection cellular anatomical structure cell leading edge plasma membrane bounded cell projection lamellipodium intracellular anatomical structure cytoplasm cytosol intracellular organelle cytoskeleton organelle membraneless organelle intracellular membraneless organelle membrane-bounded organelle cell projection cellular anatomical structure cell leading edge plasma membrane bounded cell projection lamellipodium intracellular anatomical structure cytoplasm cytosol intracellular organelle cytoskeleton organelle membraneless organelle intracellular membraneless organelle membrane-bounded organelle Golgi membrane Golgi apparatus membrane intracellular membrane-bounded organelle endomembrane system bounding membrane of organelle organelle membrane ruffle cytoplasmic ribonucleoprotein granule ribonucleoprotein granule supramolecular complex cytoplasmic stress granule microtubule organizing center centriole microtubule cytoskeleton cell periphery plasma membrane extracellular region bleb vesicle lumen intracellular vesicle membrane-enclosed lumen cytoplasmic vesicle lumen secretory granule lumen intracellular organelle lumen cytoplasmic vesicle organelle lumen secretory granule secretory vesicle vesicle Schaffer collateral - CA1 synapse synapse cell junction

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B, C, D	IPR000719	Protein kinase domain	Domain
A, B, C, D	IPR057529	MRCK/ROCK kinase, PH domain	Domain
A, B, C, D	IPR037310	Rho-associated protein kinase 1, HR1	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	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: Q13464	Prenatal Injuries malignant glioma ocular hypertension glaucoma 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. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.

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