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Yorodumi- PDB-6few: DDR1, 2-[8-(1H-indazole-5-carbonyl)-4-oxo-1-phenyl-1,3,8-triazasp... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6few | ||||||
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Title | DDR1, 2-[8-(1H-indazole-5-carbonyl)-4-oxo-1-phenyl-1,3,8-triazaspiro[4.5]decan-3-yl]-N-methylacetamide, 1.440A, P1211, Rfree=24.1% | ||||||
Components | Epithelial discoidin domain-containing receptor 1 | ||||||
Keywords | TRANSFERASE / RTK / RECEPTOR TYROSINE KINASE / COLLAGEN / DISCOIDIN DOMAIN | ||||||
Function / homology | Function and homology information protein tyrosine kinase collagen receptor activity / smooth muscle cell-matrix adhesion / regulation of extracellular matrix disassembly / regulation of cell-matrix adhesion / ear development / collagen-activated tyrosine kinase receptor signaling pathway / branching involved in mammary gland duct morphogenesis / wound healing, spreading of cells / smooth muscle cell migration / neuron projection extension ...protein tyrosine kinase collagen receptor activity / smooth muscle cell-matrix adhesion / regulation of extracellular matrix disassembly / regulation of cell-matrix adhesion / ear development / collagen-activated tyrosine kinase receptor signaling pathway / branching involved in mammary gland duct morphogenesis / wound healing, spreading of cells / smooth muscle cell migration / neuron projection extension / axon development / Non-integrin membrane-ECM interactions / mammary gland alveolus development / peptidyl-tyrosine autophosphorylation / embryo implantation / collagen binding / lactation / transmembrane receptor protein tyrosine kinase activity / regulation of cell growth / positive regulation of neuron projection development / receptor protein-tyrosine kinase / cell surface receptor protein tyrosine kinase signaling pathway / protein autophosphorylation / receptor complex / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / cell adhesion / negative regulation of cell population proliferation / extracellular space / extracellular exosome / ATP binding / metal ion binding / plasma membrane Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.44 Å | ||||||
Authors | Stihle, M. / Richter, H. / Benz, J. / Kuhn, B. / Rudolph, M.G. | ||||||
Citation | Journal: Acs Chem.Biol. / Year: 2019 Title: DNA-Encoded Library-Derived DDR1 Inhibitor Prevents Fibrosis and Renal Function Loss in a Genetic Mouse Model of Alport Syndrome. Authors: Richter, H. / Satz, A.L. / Bedoucha, M. / Buettelmann, B. / Petersen, A.C. / Harmeier, A. / Hermosilla, R. / Hochstrasser, R. / Burger, D. / Gsell, B. / Gasser, R. / Huber, S. / Hug, M.N. / ...Authors: Richter, H. / Satz, A.L. / Bedoucha, M. / Buettelmann, B. / Petersen, A.C. / Harmeier, A. / Hermosilla, R. / Hochstrasser, R. / Burger, D. / Gsell, B. / Gasser, R. / Huber, S. / Hug, M.N. / Kocer, B. / Kuhn, B. / Ritter, M. / Rudolph, M.G. / Weibel, F. / Molina-David, J. / Kim, J.J. / Santos, J.V. / Stihle, M. / Georges, G.J. / Bonfil, R.D. / Fridman, R. / Uhles, S. / Moll, S. / Faul, C. / Fornoni, A. / Prunotto, M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6few.cif.gz | 136.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6few.ent.gz | 109.6 KB | Display | PDB format |
PDBx/mmJSON format | 6few.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/fe/6few ftp://data.pdbj.org/pub/pdb/validation_reports/fe/6few | HTTPS FTP |
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-Related structure data
Related structure data | 6ferC 6fexC 6filC 6finC 6fioC 6fiqC C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 36502.855 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: DDR1, CAK, EDDR1, NEP, NTRK4, PTK3A, RTK6, TRKE / Plasmid: pFastBac1 / Cell line (production host): Sf9 / Production host: Spodoptera frugiperda (fall armyworm) References: UniProt: Q08345, receptor protein-tyrosine kinase |
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#2: Chemical | ChemComp-D6W / |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.1 Å3/Da / Density % sol: 41.33 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.5 Details: 11.5 mg/mL protein in 20mM HEPES/NaOH pH7.5, 5mM DTT, 5% glycerol, 0.1M NaCl mixed 3:1 in 600 nL with 0.1M Ca acetate, 12% PEG 8K, 0.1M Na cacodylate pH5.5 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1 / Wavelength: 1 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 16, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.44→43.42 Å / Num. obs: 53860 / % possible obs: 98.6 % / Observed criterion σ(I): -3 / Redundancy: 3.26 % / Biso Wilson estimate: 16.81 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.058 / Rrim(I) all: 0.066 / Rsym value: 0.058 / Χ2: 1.024 / Net I/σ(I): 9.34 |
Reflection shell | Resolution: 1.44→1.53 Å / Redundancy: 3.36 % / Rmerge(I) obs: 0.847 / Mean I/σ(I) obs: 0.65 / Num. unique obs: 694 / CC1/2: 1 / Rrim(I) all: 0.015 / Rsym value: 0.847 / % possible all: 99.6 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: inhouse model Resolution: 1.44→43.42 Å / SU ML: 0.24 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 29.52 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 108.04 Å2 / Biso mean: 31.1001 Å2 / Biso min: 9.89 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.44→43.42 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 19
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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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