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Open data
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Basic information
Entry | Database: PDB / ID: 2vwu | ||||||
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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. / Rowsell, S. / Packer, M. / McAlister, M. | ||||||
![]() | ![]() 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 | ![]() | 68.7 KB | Display | ![]() |
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PDB format | ![]() | 48.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 2vwvC ![]() 2vwwC ![]() 2vx0C ![]() 1jpaS C: citing same article ( S: Starting model for refinement |
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Similar structure data |
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Links
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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 598-887 / 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-7X1 / | ||
#3: Water | ChemComp-HOH / | ||
Compound details | ENGINEEREDSequence details | Y774E MUTATION NOT SEEN IN ELECTRON DENSITY | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.4 Å3/Da / Density % sol: 48.36 % / Description: NONE |
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Crystal grow | Temperature: 277 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: 4 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: ADSC CCD / Detector: CCD / Date: Nov 24, 2004 / Details: MIRRORS |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97568 Å / Relative weight: 1 |
Reflection | Resolution: 1.45→56.8 Å / Num. obs: 19173 / % possible obs: 100 % / Observed criterion σ(I): 2 / Redundancy: 7.1 % / Biso Wilson estimate: 16.18 Å2 / Rmerge(I) obs: 0.09 / Net I/σ(I): 5.44 |
Reflection shell | Resolution: 2→2.11 Å / Redundancy: 7.15 % / Rmerge(I) obs: 0.38 / Mean I/σ(I) obs: 1.6 / % possible all: 100 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 1JPA Resolution: 2→56.8 Å / Cor.coef. Fo:Fc: 0.946 / Cor.coef. Fo:Fc free: 0.935 / SU B: 7.218 / SU ML: 0.094 / Cross valid method: THROUGHOUT / σ(F): 2 / ESU R: 0.17 / ESU R Free: 0.147 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. THE FOLLOWING RESIDUES ARE DISORDERED 598 TO 608, 649 TO 653, 760 TO 781 AND 888 TO 892
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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: 23.29 Å2
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Refinement step | Cycle: LAST / Resolution: 2→56.8 Å
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Refine LS restraints |
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