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- PDB-5l6o: EphB3 kinase domain covalently bound to an irreversible inhibitor... -

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Basic information

Entry
Database: PDB / ID: 5l6o
TitleEphB3 kinase domain covalently bound to an irreversible inhibitor (compound 3)
ComponentsEphrin type-B receptor 3
KeywordsTRANSFERASE / Kinase / Irreversible Inhibitor / Quinazoline / Signaling
Function / homology
Function and homology information


urogenital system development / ephrin receptor activity / axon guidance receptor activity / regulation of cell-cell adhesion / central nervous system projection neuron axonogenesis / dendritic spine development / corpus callosum development / transmembrane-ephrin receptor activity / dendritic spine morphogenesis / axonal fasciculation ...urogenital system development / ephrin receptor activity / axon guidance receptor activity / regulation of cell-cell adhesion / central nervous system projection neuron axonogenesis / dendritic spine development / corpus callosum development / transmembrane-ephrin receptor activity / dendritic spine morphogenesis / axonal fasciculation / positive regulation of synapse assembly / EPH-Ephrin signaling / Ephrin signaling / digestive tract morphogenesis / regulation of axonogenesis / retinal ganglion cell axon guidance / regulation of GTPase activity / roof of mouth development / EPH-ephrin mediated repulsion of cells / ephrin receptor signaling pathway / EPHB-mediated forward signaling / substrate adhesion-dependent cell spreading / thymus development / axon guidance / receptor protein-tyrosine kinase / cell migration / angiogenesis / protein autophosphorylation / dendrite / extracellular region / ATP binding / plasma membrane / cytosol
Similarity search - Function
Ephrin type-B receptor 3, ligand binding 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 3, ligand binding 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 / 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
1-(4-phenylazanylquinazolin-7-yl)ethanone / 1,4-DIETHYLENE DIOXIDE / Ephrin type-B receptor 3
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.88 Å
AuthorsSchimpl, M. / Overman, R. / Kung, A. / Chen, Y.-C. / Ni, F. / Zhu, J. / Turner, M. / Molina, H. / Zhang, C.
Funding support United States, 2items
OrganizationGrant numberCountry
National Science FoundationCHE-1455306 United States
American Cancer SocietyIRG-58-007-51 United States
CitationJournal: J.Am.Chem.Soc. / Year: 2016
Title: Development of Specific, Irreversible Inhibitors for a Receptor Tyrosine Kinase EphB3.
Authors: Kung, A. / Chen, Y.C. / Schimpl, M. / Ni, F. / Zhu, J. / Turner, M. / Molina, H. / Overman, R. / Zhang, C.
History
DepositionMay 30, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 10, 2016Provider: repository / Type: Initial release
Revision 1.1Sep 7, 2016Group: Database references
Revision 1.2Jan 10, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Ephrin type-B receptor 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,1173
Polymers33,7661
Non-polymers3512
Water1,69394
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area280 Å2
ΔGint5 kcal/mol
Surface area13220 Å2
MethodPISA
Unit cell
Length a, b, c (Å)46.817, 57.214, 113.184
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Ephrin type-B receptor 3 / EPH-like tyrosine kinase 2 / EPH-like kinase 2 / Embryonic kinase 2 / hEK2 / Tyrosine-protein kinase TYRO6


Mass: 33765.711 Da / Num. of mol.: 1 / Mutation: A899P
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: EPHB3, ETK2, HEK2, TYRO6 / Production host: Escherichia coli (E. coli)
References: UniProt: P54753, receptor protein-tyrosine kinase
#2: Chemical ChemComp-6P6 / 1-(4-phenylazanylquinazolin-7-yl)ethanone


Mass: 263.294 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C16H13N3O
#3: Chemical ChemComp-DIO / 1,4-DIETHYLENE DIOXIDE


Mass: 88.105 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H8O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 94 / Source method: isolated from a natural source / Formula: H2O

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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: 2.26 Å3/Da / Density % sol: 45.58 % / Description: plate
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5 / Details: 1,4-dioxane, Tris buffer, magnesium chloride

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.97949 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jan 23, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97949 Å / Relative weight: 1
ReflectionResolution: 1.88→57.21 Å / Num. obs: 25671 / % possible obs: 100 % / Redundancy: 6.2 % / Biso Wilson estimate: 37.27 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.049 / Net I/σ(I): 17.6
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsDiffraction-ID% possible all
1.88-1.984.80.5482.51100
5.93-57.215.70.035199.7

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
BUSTER2.11.6refinement
Aimless0.5.17data scaling
MOLREPphasing
PDB_EXTRACT3.2data extraction
XDSdata reduction
XDSdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3ZFY

3zfy


Resolution: 1.88→56.59 Å / Cor.coef. Fo:Fc: 0.947 / Cor.coef. Fo:Fc free: 0.94 / Rfactor Rfree error: 0 / SU R Cruickshank DPI: 0.129 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.131 / SU Rfree Blow DPI: 0.114 / SU Rfree Cruickshank DPI: 0.113
RfactorNum. reflection% reflectionSelection details
Rfree0.206 1219 4.79 %RANDOM
Rwork0.189 ---
obs0.19 25443 100 %-
Displacement parametersBiso mean: 68.56 Å2
Baniso -1Baniso -2Baniso -3
1-3.2447 Å20 Å20 Å2
2--6.6717 Å20 Å2
3----9.9164 Å2
Refine analyzeLuzzati coordinate error obs: 0.22 Å
Refinement stepCycle: LAST / Resolution: 1.88→56.59 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2071 0 26 94 2191
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.012162HARMONIC2
X-RAY DIFFRACTIONt_angle_deg0.932949HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d738SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes49HARMONIC2
X-RAY DIFFRACTIONt_gen_planes311HARMONIC5
X-RAY DIFFRACTIONt_it2162HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion2.79
X-RAY DIFFRACTIONt_other_torsion16.51
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion279SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact2570SEMIHARMONIC4
LS refinement shellResolution: 1.88→1.96 Å / Rfactor Rfree error: 0 / Total num. of bins used: 13
RfactorNum. reflection% reflection
Rfree0.222 146 5.17 %
Rwork0.208 2680 -
all0.209 2826 -
obs--99.93 %
Refinement TLS params.Method: refined / Origin x: 12.4171 Å / Origin y: -4.5503 Å / Origin z: -16.61 Å
111213212223313233
T-0.1772 Å20.0837 Å2-0.1717 Å2--0.2718 Å2-0.1032 Å2---0.1978 Å2
L2.9389 °2-1.3016 °20.0024 °2-5.1546 °20.3298 °2--1.9175 °2
S-0.3594 Å °-0.4396 Å °0.3545 Å °1.0034 Å °0.4489 Å °-0.7752 Å °0.0316 Å °0.1807 Å °-0.0895 Å °
Refinement TLS groupSelection details: { A|* }

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