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Open data
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Basic information
Entry | Database: PDB / ID: 2vx1 | ||||||
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Title | ephB4 kinase domain inhibitor complex | ||||||
![]() | EPHRIN TYPE-B RECEPTOR 4 | ||||||
![]() | TRANSFERASE / TYROSINE-PROTEIN KINASE / RECEPTOR TYROSINE KINASE / KINASE / MUTANT / MEMBRANE / RECEPTOR / ATP-BINDING / POLYMORPHISM / GLYCOPROTEIN / TRANSMEMBRANE / PHOSPHOPROTEIN / UNPHOSPHORYLATED / NUCLEOTIDE-BINDING | ||||||
Function / homology | ![]() ephrin receptor activity / cell migration involved in sprouting angiogenesis / EPH-Ephrin signaling / Ephrin signaling / EPH-ephrin mediated repulsion of cells / ephrin receptor signaling pathway / transmembrane receptor protein tyrosine kinase activity / heart morphogenesis / EPHB-mediated forward signaling / 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 / transmembrane receptor protein tyrosine kinase activity / heart morphogenesis / EPHB-mediated forward signaling / 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 | ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Read, J. / Brassington, C.A. / Green, I. / McCall, E.J. / Valentine, A.L. / Barratt, D. / Leach, A.G. / Kettle, J.G. | ||||||
![]() | ![]() Title: Inhibitors of the Tyrosine Kinase Ephb4. Part 2: Structure-Based Discovery and Optimisation of 3,5-Bis Substituted Anilinopyrimidines. Authors: Bardelle, C. / Coleman, T. / 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. #1: ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 77.8 KB | Display | ![]() |
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PDB format | ![]() | 55.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 2vwxC ![]() 2vwyC ![]() 2vwzC ![]() 2vwuS S: Starting model for refinement C: citing same article ( |
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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: 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.) ![]() ![]() ![]() References: UniProt: P54760, receptor protein-tyrosine kinase | ||||||
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#2: Chemical | ChemComp-7X8 / | ||||||
#3: Chemical | #4: Water | ChemComp-HOH / | Compound details | ENGINEERED | Sequence details | Y774E MUTATION NOT SEEN IN ELECTRON DENSITY | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.08 Å3/Da / Density % sol: 40.3 % / Description: NONE |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: 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: ![]() |
Detector | Type: RIGAKU-MSC / Detector: CCD / Date: Nov 22, 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: 1.65→100 Å / Num. obs: 28794 / % possible obs: 85.2 % / Observed criterion σ(I): 2 / Redundancy: 3.3 % / Biso Wilson estimate: 17.8 Å2 / Rmerge(I) obs: 0.07 / Net I/σ(I): 10.1 |
Reflection shell | Resolution: 1.65→1.71 Å / Redundancy: 1.96 % / Rmerge(I) obs: 0.36 / Mean I/σ(I) obs: 2 / % possible all: 27.5 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 2VWU Resolution: 1.65→57.45 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.938 / SU B: 3.852 / SU ML: 0.06 / Cross valid method: THROUGHOUT / ESU R: 0.114 / ESU R Free: 0.112 / 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 / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 19.122 Å2
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Refinement step | Cycle: LAST / Resolution: 1.65→57.45 Å
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