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Yorodumi- PDB-8gds: CRYSTAL STRUCTURE OF RHO-ASSOCIATED PROTEIN KINASE 2 (ROCK2) IN C... -
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-Basic information
Entry | Database: PDB / ID: 8gds | ||||||
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Title | CRYSTAL STRUCTURE OF RHO-ASSOCIATED PROTEIN KINASE 2 (ROCK2) IN COMPLEX WITH 4-(4-(2-(2,3-DIHYDRO-1H- INDOL-1-YL)-2-OXOETHYL)PHENYL)-1(2H)-PHTHALAZINONE | ||||||
Components | Rho-associated protein kinase 2 | ||||||
Keywords | TRANSFERASE / ROCK-2 / RHO KINASE 2 / RHO-ASSOCIATED / COILED-COIL-CONTAINING PROTEIN KINASE II / kinase / ligand inhibitor | ||||||
Function / homology | Function and homology information cellular response to acetylcholine / positive regulation of connective tissue growth factor production / positive regulation of amyloid precursor protein catabolic process / positive regulation of centrosome duplication / regulation of angiotensin-activated signaling pathway / Rho-dependent protein serine/threonine kinase activity / negative regulation of protein localization to lysosome / regulation of keratinocyte differentiation / positive regulation of connective tissue replacement / positive regulation of fibroblast growth factor production ...cellular response to acetylcholine / positive regulation of connective tissue growth factor production / positive regulation of amyloid precursor protein catabolic process / positive regulation of centrosome duplication / regulation of angiotensin-activated signaling pathway / Rho-dependent protein serine/threonine kinase activity / negative regulation of protein localization to lysosome / regulation of keratinocyte differentiation / positive regulation of connective tissue replacement / positive regulation of fibroblast growth factor production / positive regulation of aspartic-type endopeptidase activity involved in amyloid precursor protein catabolic process / response to transforming growth factor beta / negative regulation of myosin-light-chain-phosphatase activity / regulation of nervous system process / regulation of cell junction assembly / negative regulation of bicellular tight junction assembly / regulation of protein metabolic process / modulation by host of viral process / regulation of cellular response to hypoxia / positive regulation of protein localization to early endosome / embryonic morphogenesis / negative regulation of nitric oxide biosynthetic process / negative regulation of biomineral tissue development / cellular response to testosterone stimulus / actomyosin structure organization / regulation of establishment of endothelial barrier / RHO GTPases Activate ROCKs / regulation of stress fiber assembly / regulation of cell motility / Sema4D induced cell migration and growth-cone collapse / aortic valve morphogenesis / response to angiotensin / regulation of establishment of cell polarity / RHOBTB1 GTPase cycle / cortical actin cytoskeleton organization / regulation of focal adhesion assembly / RHOB GTPase cycle / positive regulation of amyloid-beta formation / tau-protein kinase activity / EPHA-mediated growth cone collapse / mRNA destabilization / positive regulation of cardiac muscle hypertrophy / RHOC GTPase cycle / RHOH GTPase cycle / centrosome duplication / mitotic cytokinesis / Rho protein signal transduction / smooth muscle contraction / RHOA GTPase cycle / epithelial to mesenchymal transition / canonical NF-kappaB signal transduction / regulation of cell adhesion / positive regulation of stress fiber assembly / EPHB-mediated forward signaling / blood vessel diameter maintenance / negative regulation of angiogenesis / positive regulation of endothelial cell migration / response to ischemia / protein localization to plasma membrane / regulation of actin cytoskeleton organization / peptidyl-threonine phosphorylation / tau protein binding / regulation of circadian rhythm / cytoplasmic ribonucleoprotein granule / small GTPase binding / VEGFA-VEGFR2 Pathway / rhythmic process / G alpha (12/13) signalling events / actin cytoskeleton organization / peptidyl-serine phosphorylation / Potential therapeutics for SARS / positive regulation of MAPK cascade / cytoskeleton / non-specific serine/threonine protein kinase / positive regulation of cell migration / positive regulation of protein phosphorylation / negative regulation of gene expression / protein phosphorylation / protein serine kinase activity / protein serine/threonine kinase activity / centrosome / positive regulation of gene expression / structural molecule activity / RNA binding / ATP binding / metal ion binding / nucleus / plasma membrane / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.71 Å | ||||||
Authors | Muckelbauer, J.K. | ||||||
Funding support | United States, 1items
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Citation | Journal: Bioorg.Med.Chem.Lett. / Year: 2023 Title: Phthalazinone-based lactams and cyclic ureas as ROCK2 selective inhibitors. Authors: Hu, Z. / Sitkoff, D. / Glunz, P.W. / Zou, Y. / Wang, C. / Muckelbauer, J.K. / Adam, L.P. / Wexler, R.R. / Quan, M.L. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8gds.cif.gz | 302.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8gds.ent.gz | 246.7 KB | Display | PDB format |
PDBx/mmJSON format | 8gds.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/gd/8gds ftp://data.pdbj.org/pub/pdb/validation_reports/gd/8gds | HTTPS FTP |
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-Related structure data
Similar structure data | Similarity search - Function & homologyF&H Search |
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-Links
-Assembly
Deposited unit |
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1 |
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2 |
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3 |
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4 |
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Unit cell |
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-Components
#1: Protein | Mass: 45471.727 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: ROCK2, KIAA0619 / Production host: Trichoplusia ni (cabbage looper) References: UniProt: O75116, non-specific serine/threonine protein kinase #2: Chemical | ChemComp-Z8O / #3: Chemical | ChemComp-SO4 / #4: Water | ChemComp-HOH / | Has ligand of interest | Y | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.79 Å3/Da / Density % sol: 67.52 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / Details: NULL |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 15, 2012 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.71→98.03 Å / Num. obs: 52361 / % possible obs: 87.5 % / Redundancy: 2.9 % / CC1/2: 0.989 / Rpim(I) all: 0.09 / Net I/σ(I): 6.1 |
Reflection shell | Resolution: 2.71→2.93 Å / Redundancy: 3.5 % / Mean I/σ(I) obs: 1.4 / Num. unique obs: 2618 / CC1/2: 0.555 / Rpim(I) all: 0.513 / % possible all: 61 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.71→98.03 Å / Cor.coef. Fo:Fc: 0.895 / Cor.coef. Fo:Fc free: 0.855 / SU R Cruickshank DPI: 1.195 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 1.034 / SU Rfree Blow DPI: 0.354 / SU Rfree Cruickshank DPI: 0.364
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Displacement parameters | Biso mean: 52.85 Å2
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Refine analyze | Luzzati coordinate error obs: 0.43 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.71→98.03 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.71→2.9 Å / Total num. of bins used: 29
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