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- PDB-4bb4: ephB4 kinase domain inhibitor complex -

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Basic information

Entry
Database: PDB / ID: 4bb4
TitleephB4 kinase domain inhibitor complex
ComponentsEPHRIN TYPE-B RECEPTOR 4
KeywordsTRANSFERASE / UNPHOSPHORYLATED
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
Ephrin type-B receptor 4, ligand binding domain / EPH-B4, SAM domain / Tyrosine-protein kinase ephrin type A/B receptor-like / Tyrosine-protein kinase ephrin type A/B receptor-like / Ephrin receptor type-A /type-B / Ephrin receptor ligand binding domain / Tyrosine-protein kinase, receptor class V, conserved site / Ephrin receptor, transmembrane domain / Ephrin receptor ligand binding domain / Ephrin type-A receptor 2 transmembrane domain ...Ephrin type-B receptor 4, ligand binding domain / EPH-B4, SAM domain / Tyrosine-protein kinase ephrin type A/B receptor-like / Tyrosine-protein kinase ephrin type A/B receptor-like / Ephrin receptor type-A /type-B / Ephrin receptor ligand binding domain / Tyrosine-protein kinase, receptor class V, conserved site / Ephrin receptor, transmembrane domain / Ephrin receptor ligand binding domain / Ephrin type-A receptor 2 transmembrane domain / Receptor tyrosine kinase class V signature 1. / Receptor tyrosine kinase class V signature 2. / Eph receptor ligand-binding domain profile. / Ephrin receptor ligand binding domain / Putative ephrin-receptor like / SAM domain (Sterile alpha motif) / SAM domain profile. / Sterile alpha motif. / Sterile alpha motif domain / Sterile alpha motif/pointed domain superfamily / Growth factor receptor cysteine-rich domain superfamily / EGF-like domain signature 2. / Fibronectin type III domain / Fibronectin type 3 domain / Fibronectin type-III domain profile. / Galactose-binding-like domain superfamily / Fibronectin type III / Fibronectin type III superfamily / Tyrosine-protein kinase, catalytic domain / Tyrosine kinase, catalytic domain / Tyrosine protein kinases specific active-site signature. / Tyrosine-protein kinase, active site / Protein tyrosine and serine/threonine kinase / Serine-threonine/tyrosine-protein kinase, catalytic domain / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); domain 1 / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; domain 1 / Protein kinase, ATP binding site / Protein kinases ATP-binding region signature. / Immunoglobulin-like fold / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily / 2-Layer Sandwich / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Chem-32W / Ephrin type-B receptor 4
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.65 Å
AuthorsRead, J. / Brassington, C.A. / Green, I. / McCall, E.J. / Valentine, A.L.
CitationJournal: J.Med.Chem. / Year: 2013
Title: Discovery and Optimization of a Novel Series of Potent Mutant B-Raf V600E Selective Kinase Inhibitors.
Authors: Vasbinder, M.M. / Aquila, B. / Augustin, M. / Chen, H. / Cheung, T. / Cook, D. / Drew, L. / Fauber, B.P. / Glossop, S. / Grondine, M. / Hennessy, E.J. / Johannes, J. / Lee, S. / Lyne, P.D. / ...Authors: Vasbinder, M.M. / Aquila, B. / Augustin, M. / Chen, H. / Cheung, T. / Cook, D. / Drew, L. / Fauber, B.P. / Glossop, S. / Grondine, M. / Hennessy, E.J. / Johannes, J. / Lee, S. / Lyne, P.D. / Mortl, M. / Omer, C. / Palakurthi, S. / Pontz, T. / Read, J. / Sha, L. / Shen, M. / Steinbacher, S. / Wang, H. / Wu, A. / Ye, M.
History
DepositionSep 19, 2012Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 27, 2013Provider: repository / Type: Initial release
Revision 1.1Apr 10, 2013Group: Database references / Derived calculations
Revision 1.2Apr 4, 2018Group: Data collection / Category: diffrn_source / Item: _diffrn_source.type
Revision 1.3Apr 24, 2019Group: Data collection / Source and taxonomy / Category: entity_src_gen / Item: _entity_src_gen.pdbx_host_org_cell_line

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: EPHRIN TYPE-B RECEPTOR 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,3834
Polymers33,9351
Non-polymers4483
Water4,216234
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)46.421, 53.329, 61.209
Angle α, β, γ (deg.)90.00, 111.50, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein EPHRIN TYPE-B RECEPTOR 4 / EPHB4 RECEPTOR TYROSINE KINASE / HEPATOMA TRANSMEMBRANE KINASE / TYROSINE-PROTEIN KINASE TYRO11


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
#2: Chemical ChemComp-32W / N-(2-methoxyethyl)-4-[(6-pyridin-4-ylquinazolin-2-yl)amino]benzamide


Mass: 399.445 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C23H21N5O2
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 234 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsY774E MUTATION NOT SEEN IN ELECTRON DENSITY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.08 Å3/Da / Density % sol: 40.79 % / Description: NONE
Crystal growpH: 7.4 / Details: pH 7.4

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E / Wavelength: 1.5418
DetectorType: RIGAKU CCD / Detector: CCD / Date: May 2, 2006 / Details: MIRRORS
RadiationMonochromator: NI FILTER / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.65→100 Å / Num. obs: 29124 / % possible obs: 86.7 % / Observed criterion σ(I): 2 / Redundancy: 3.27 % / Biso Wilson estimate: 30.89 Å2 / Rmerge(I) obs: 0.04 / Net I/σ(I): 13.2
Reflection shellResolution: 1.65→1.7 Å / Redundancy: 1.7 % / Rmerge(I) obs: 0.36 / Mean I/σ(I) obs: 1.8 / % possible all: 33.4

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Processing

Software
NameVersionClassification
BUSTER-TNT2.11.2refinement
d*TREKdata reduction
d*TREKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.65→21.28 Å / Cor.coef. Fo:Fc: 0.9481 / Cor.coef. Fo:Fc free: 0.9432 / Cross valid method: THROUGHOUT / σ(F): 2 / Details: REMARK 3
RfactorNum. reflection% reflectionSelection details
Rfree0.2361 1469 5 %RANDOM
Rwork0.2072 ---
obs0.2087 29124 86.68 %-
Displacement parametersBiso mean: 39.15 Å2
Baniso -1Baniso -2Baniso -3
1-0.7676 Å20 Å23.3102 Å2
2--1.8795 Å20 Å2
3----2.6471 Å2
Refine analyzeLuzzati coordinate error obs: 0.284 Å
Refinement stepCycle: LAST / Resolution: 1.65→21.28 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2047 0 32 234 2313
LS refinement shellResolution: 1.65→1.71 Å / Total num. of bins used: 15
RfactorNum. reflection% reflection
Rfree0.3672 63 5.81 %
Rwork0.2763 1022 -
all0.2815 1085 -
obs--33.4 %

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