+Open data
-Basic information
Entry | Database: PDB / ID: 2vww | ||||||
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Title | ephB4 kinase domain inhibitor complex | ||||||
Components | EPHRIN TYPE-B RECEPTOR 4 | ||||||
Keywords | TRANSFERASE / TYROSINE-PROTEIN KINASE / RECEPTOR TYROSINE KINASE / KINASE / MUTANT / MEMBRANE / RECEPTOR / ATP-BINDING / POLYMORPHISM / GLYCOPROTEIN / TRANSMEMBRANE / PHOSPHOPROTEIN / UNPHOSPHORYLATED / NUCLEOTIDE-BINDING | ||||||
Function / homology | Function and homology information ephrin receptor activity / cell migration involved in sprouting angiogenesis / EPH-Ephrin signaling / Ephrin signaling / EPH-ephrin mediated repulsion of cells / ephrin receptor signaling pathway / heart morphogenesis / EPHB-mediated forward signaling / transmembrane receptor protein tyrosine kinase activity / receptor protein-tyrosine kinase ...ephrin receptor activity / cell migration involved in sprouting angiogenesis / EPH-Ephrin signaling / Ephrin signaling / EPH-ephrin mediated repulsion of cells / ephrin receptor signaling pathway / heart morphogenesis / EPHB-mediated forward signaling / transmembrane receptor protein tyrosine kinase activity / receptor protein-tyrosine kinase / angiogenesis / protein autophosphorylation / receptor complex / cell adhesion / extracellular exosome / extracellular region / ATP binding / plasma membrane / cytosol Similarity search - Function | ||||||
Biological species | HOMO SAPIENS (human) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.9 Å | ||||||
Authors | Read, J. / Brassington, C.A. / Green, I. / McCall, E.J. / Valentine, A.L. / Barratt, D. / Leach, A.G. / Kettle, J.G. | ||||||
Citation | Journal: Bioorg.Med.Chem.Lett. / Year: 2008 Title: Inhibitors of the Tyrosine Kinase Ephb4. Part 1: Structure-Based Design and Optimization of a Series of 2,4-Bis-Anilinopyrimidines Authors: Bardelle, C. / Cross, D. / Davenport, S. / Kettle, J.G. / Ko, E.J. / Leach, A.G. / Mortlock, A. / Read, J. / Roberts, N.J. / Robins, P. / Williams, E.J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2vww.cif.gz | 68.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2vww.ent.gz | 48.6 KB | Display | PDB format |
PDBx/mmJSON format | 2vww.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/vw/2vww ftp://data.pdbj.org/pub/pdb/validation_reports/vw/2vww | HTTPS FTP |
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-Related structure data
Related structure data | 2vwuSC 2vwvC 2vx0C C: citing same article (ref.) S: Starting model for refinement |
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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: 33934.816 Da / Num. of mol.: 1 / Fragment: KINASE DOMAIN, RESIDUES 598-899 / Mutation: YES Source method: isolated from a genetically manipulated source Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PFASTBAC / Cell line (production host): Sf21 / Production host: SPODOPTERA FRUGIPERDA (fall armyworm) References: UniProt: P54760, receptor protein-tyrosine kinase | ||
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#2: Chemical | ChemComp-7X2 / | ||
#3: Water | ChemComp-HOH / | ||
Compound details | ENGINEEREDSequence details | Y774E MUTATION NOT SEEN IN ELECTRON DENSITY | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.3 Å3/Da / Density % sol: 44 % / Description: NONE |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: CRYSTALLIZATION CONDITIONS: PROTEIN\: 12MG/ML IN 50MM MOPS PH 6.5, 50MM NACL, 1MM DTT RESERVOIR\: 25% PEG 5000 MME, 0.1M TRIS PH 7.5, 0.15M MGCL2, 15% GLYCEROL TEMP\:18 DEGREES C SITTING ...Details: CRYSTALLIZATION CONDITIONS: PROTEIN\: 12MG/ML IN 50MM MOPS PH 6.5, 50MM NACL, 1MM DTT RESERVOIR\: 25% PEG 5000 MME, 0.1M TRIS PH 7.5, 0.15M MGCL2, 15% GLYCEROL TEMP\:18 DEGREES C SITTING DROP\: 2 UL PROTEIN, 0.6 UL RESERVOIR |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU MICROMAX-007 / Wavelength: 1.5418 |
Detector | Type: RIGAKU-MSC SATURN / Detector: CCD / Date: Jun 10, 2005 / Details: MIRRORS |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→17.21 Å / Num. obs: 17968 / % possible obs: 95.5 % / Observed criterion σ(I): 2 / Redundancy: 2.13 % / Biso Wilson estimate: 20.68 Å2 / Rmerge(I) obs: 0.06 / Net I/σ(I): 10.74 |
Reflection shell | Resolution: 1.9→1.92 Å / Redundancy: 93.6 % / Rmerge(I) obs: 0.38 / Mean I/σ(I) obs: 1.9 / % possible all: 93.6 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2VWU Resolution: 1.9→19.3 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.933 / SU B: 7.44 / SU ML: 0.1 / Cross valid method: THROUGHOUT / σ(F): 2 / ESU R: 0.191 / ESU R Free: 0.168 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
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Solvent computation | Ion probe radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL PLUS MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 30.52 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.9→19.3 Å
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