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- PDB-6fnm: Crystal Structure of Ephrin B4 (EphB4) Receptor Protein Kinase wi... -

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Basic information

Entry
Database: PDB / ID: 6fnm
TitleCrystal Structure of Ephrin B4 (EphB4) Receptor Protein Kinase with Dasatinib
ComponentsEphrin type-B receptor 4
KeywordsTRANSFERASE / Inhibitor / Complex / Protein Tyrosine Kinase
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 / protein autophosphorylation / angiogenesis / 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-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 / Fibronectin type III domain / Growth factor receptor cysteine-rich domain superfamily / EGF-like domain signature 2. / 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 / Serine-threonine/tyrosine-protein kinase, catalytic domain / Protein tyrosine and serine/threonine kinase / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; domain 1 / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); 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-1N1 / Ephrin type-B receptor 4
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.157 Å
AuthorsKudlinzki, D. / Troester, A. / Witt, K. / Linhard, V.L. / Saxena, K. / Schwalbe, H.
Funding support Germany, 1items
OrganizationGrant numberCountry
DKTKL590 Germany
CitationJournal: ChemMedChem / Year: 2018
Title: NVP-BHG712: Effects of Regioisomers on the Affinity and Selectivity toward the EPHrin Family.
Authors: Troster, A. / Heinzlmeir, S. / Berger, B.T. / Gande, S.L. / Saxena, K. / Sreeramulu, S. / Linhard, V. / Nasiri, A.H. / Bolte, M. / Muller, S. / Kuster, B. / Medard, G. / Kudlinzki, D. / Schwalbe, H.
History
DepositionFeb 4, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 8, 2018Provider: repository / Type: Initial release
Revision 1.1Aug 29, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Jan 17, 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 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,9762
Polymers33,4881
Non-polymers4881
Water6,395355
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, Monomeric Kinase Domain with bound Inhibitor
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area800 Å2
ΔGint-4 kcal/mol
Surface area13880 Å2
MethodPISA
Unit cell
Length a, b, c (Å)45.941, 54.111, 62.162
Angle α, β, γ (deg.)90.00, 110.45, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Ephrin type-B receptor 4 / Hepatoma transmembrane kinase / Tyrosine-protein kinase TYRO11


Mass: 33488.359 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: EPHB4, HTK, MYK1, TYRO11 / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: P54760, receptor protein-tyrosine kinase
#2: Chemical ChemComp-1N1 / N-(2-CHLORO-6-METHYLPHENYL)-2-({6-[4-(2-HYDROXYETHYL)PIPERAZIN-1-YL]-2-METHYLPYRIMIDIN-4-YL}AMINO)-1,3-THIAZOLE-5-CARBOXAMIDE / Dasatinib


Mass: 488.006 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C22H26ClN7O2S / Comment: medication*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 355 / 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: 2.1 Å3/Da / Density % sol: 41.5 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 25 % PEG5000 MME, 15 % Glycerol, 0.15 M MgCl2, 0.1 M TRIS pH7.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.9184 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jan 17, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9184 Å / Relative weight: 1
ReflectionResolution: 1.157→43.044 Å / Num. obs: 98097 / % possible obs: 97.5 % / Redundancy: 3.69 % / Biso Wilson estimate: 20.95 Å2 / CC1/2: 0.998 / Rrim(I) all: 0.068 / Net I/σ(I): 9.9
Reflection shellResolution: 1.157→1.22 Å / Redundancy: 3.42 % / Mean I/σ(I) obs: 0.31 / Num. unique obs: 14620 / CC1/2: 0.121 / % possible all: 90.2

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155)refinement
XDSXDSapp 2.0data reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2VWU

2vwu


Resolution: 1.157→43.044 Å / SU ML: 0.21 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 26.71
RfactorNum. reflection% reflection
Rfree0.1945 2077 2.14 %
Rwork0.1838 --
obs0.1837 96998 97.52 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.157→43.044 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2149 0 33 355 2537
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0082388
X-RAY DIFFRACTIONf_angle_d1.1383243
X-RAY DIFFRACTIONf_dihedral_angle_d16.8121486
X-RAY DIFFRACTIONf_chiral_restr0.085336
X-RAY DIFFRACTIONf_plane_restr0.006427
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.157-1.18390.58111140.57765304X-RAY DIFFRACTION82
1.1839-1.21350.44081370.43136210X-RAY DIFFRACTION96
1.2135-1.24630.33531380.34716300X-RAY DIFFRACTION98
1.2463-1.2830.33751410.32636434X-RAY DIFFRACTION100
1.283-1.32440.33241400.32036396X-RAY DIFFRACTION99
1.3244-1.37180.26141410.26076428X-RAY DIFFRACTION99
1.3718-1.42670.21291390.21686343X-RAY DIFFRACTION98
1.4267-1.49160.22671370.19726260X-RAY DIFFRACTION97
1.4916-1.57030.19891410.18016448X-RAY DIFFRACTION100
1.5703-1.66870.19151410.17186462X-RAY DIFFRACTION100
1.6687-1.79750.19871420.16836484X-RAY DIFFRACTION100
1.7975-1.97840.18151410.17436426X-RAY DIFFRACTION99
1.9784-2.26470.18081390.16916385X-RAY DIFFRACTION98
2.2647-2.85320.20541430.17426515X-RAY DIFFRACTION99
2.8532-43.07410.15491430.15226525X-RAY DIFFRACTION98

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