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Open data
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Basic information
Entry | Database: PDB / ID: 4yve | ||||||
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Title | ROCK 1 bound to methoxyphenyl thiazole inhibitor | ||||||
![]() | Rho-associated protein kinase 1 | ||||||
![]() | TRANSFERASE/TRANSFERASE INHIBITOR / kinase / dimer / dimerization / myosin / TRANSFERASE-TRANSFERASE INHIBITOR complex | ||||||
Function / homology | ![]() regulation of angiotensin-activated signaling pathway / apical constriction / Rho-dependent protein serine/threonine kinase activity / podocyte cell migration / positive regulation of phosphatase activity / myoblast migration / positive regulation of connective tissue replacement / membrane to membrane docking / negative regulation of membrane protein ectodomain proteolysis / regulation of keratinocyte differentiation ...regulation of angiotensin-activated signaling pathway / apical constriction / Rho-dependent protein serine/threonine kinase activity / podocyte cell migration / positive regulation of phosphatase activity / myoblast migration / positive regulation of connective tissue replacement / membrane to membrane docking / negative regulation of membrane protein ectodomain proteolysis / regulation of keratinocyte differentiation / response to transforming growth factor beta / negative regulation of myosin-light-chain-phosphatase activity / regulation of cell junction assembly / positive regulation of dephosphorylation / negative regulation of bicellular tight junction assembly / bleb / regulation of synapse maturation / negative regulation of amyloid precursor protein catabolic process / neuron projection arborization / bleb assembly / embryonic morphogenesis / leukocyte tethering or rolling / negative regulation of biomineral tissue development / negative regulation of phosphorylation / positive regulation of amyloid-beta clearance / regulation of establishment of endothelial barrier / RHO GTPases Activate ROCKs / negative regulation of motor neuron apoptotic process / regulation of stress fiber assembly / regulation of cell motility / actomyosin structure organization / Sema4D induced cell migration and growth-cone collapse / aortic valve morphogenesis / response to angiotensin / regulation of establishment of cell polarity / RHOBTB1 GTPase cycle / regulation of synaptic vesicle endocytosis / motor neuron apoptotic process / RND3 GTPase cycle / cortical actin cytoskeleton organization / regulation of neuron differentiation / regulation of focal adhesion assembly / leukocyte cell-cell adhesion / RHOB GTPase cycle / tau-protein kinase activity / leukocyte migration / EPHA-mediated growth cone collapse / mRNA destabilization / positive regulation of cardiac muscle hypertrophy / Apoptotic cleavage of cellular proteins / RHOC GTPase cycle / negative regulation of amyloid-beta formation / positive regulation of focal adhesion assembly / RHOH GTPase cycle / Rho protein signal transduction / mitotic cytokinesis / smooth muscle contraction / RHOA GTPase cycle / epithelial to mesenchymal transition / canonical NF-kappaB signal transduction / regulation of cell adhesion / positive regulation of autophagy / regulation of microtubule cytoskeleton organization / regulation of cell migration / ruffle / EPHB-mediated forward signaling / centriole / blood vessel diameter maintenance / negative regulation of angiogenesis / negative regulation of protein binding / protein localization to plasma membrane / regulation of actin cytoskeleton organization / Schaffer collateral - CA1 synapse / tau protein binding / small GTPase binding / VEGFA-VEGFR2 Pathway / cytoplasmic stress granule / neuron projection development / G alpha (12/13) signalling events / lamellipodium / actin cytoskeleton organization / peptidyl-serine phosphorylation / secretory granule lumen / Potential therapeutics for SARS / positive regulation of MAPK cascade / cytoskeleton / non-specific serine/threonine protein kinase / protein kinase activity / Golgi membrane / protein phosphorylation / protein serine kinase activity / protein serine/threonine kinase activity / Neutrophil degranulation / positive regulation of gene expression / signal transduction / extracellular region / ATP binding / metal ion binding / plasma membrane / cytoplasm Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Jacobs, M.D. | ||||||
![]() | ![]() Title: Design, Synthesis, and Structure-Activity Relationships of Pyridine-Based Rho Kinase (ROCK) Inhibitors. Authors: Green, J. / Cao, J. / Bandarage, U.K. / Gao, H. / Court, J. / Marhefka, C. / Jacobs, M. / Taslimi, P. / Newsome, D. / Nakayama, T. / Shah, S. / Rodems, S. #1: ![]() Title: The structure of dimeric ROCK I reveals the mechanism for ligand selectivity. Authors: Jacobs, M. / Hayakawa, K. / Swenson, L. / Bellon, S. / Fleming, M. / Taslimi, P. / Doran, J. #2: ![]() Title: ROCK inhibitors 2. Improving potency, selectivity and solubility through the application of rationally designed solubilizing groups. Authors: Gao, H. / Marhefka, C. / Jacobs, M.D. / Cao, J. / Bandarage, U.K. / Green, J. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 335.3 KB | Display | ![]() |
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PDB format | ![]() | 278.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 884 KB | Display | ![]() |
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Full document | ![]() | 896.8 KB | Display | |
Data in XML | ![]() | 29.1 KB | Display | |
Data in CIF | ![]() | 39.5 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 4yvcC ![]() 5bmlC ![]() 2etrS C: citing same article ( S: Starting model for refinement |
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Similar structure data |
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 48012.285 Da / Num. of mol.: 2 / Fragment: N-terminal kinase domain (UNP residues 6-415) Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() References: UniProt: Q13464, non-specific serine/threonine protein kinase #2: Chemical | #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 4.51 Å3/Da / Density % sol: 72.71 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5.5 Details: 0.45 mM protein, 5% PEG3350, 100 mM MES, 50 mM calcium chloride, 10 mM DTT |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: ![]() ![]() ![]() | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Jan 28, 2003 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1.1 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 3.4→29.78 Å / Num. obs: 23765 / % possible obs: 99 % / Redundancy: 7.41 % / Biso Wilson estimate: 94.4 Å2 / Rmerge(I) obs: 0.155 / Χ2: 2.29 / Net I/σ(I): 4.2 / Num. measured all: 178283 / Scaling rejects: 2109 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB entry 2ETR Resolution: 3.4→19.86 Å / Cor.coef. Fo:Fc: 0.9051 / Cor.coef. Fo:Fc free: 0.8771 / Cross valid method: THROUGHOUT / σ(F): 0 / SU Rfree Blow DPI: 0.427
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Displacement parameters | Biso max: 184.88 Å2 / Biso mean: 85.88 Å2 / Biso min: 20 Å2
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Refine analyze | Luzzati coordinate error obs: 0.728 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 3.4→19.86 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 3.4→3.55 Å / Total num. of bins used: 12
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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