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- PDB-4aw5: Complex of the EphB4 kinase domain with an oxindole inhibitor -

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Basic information

Entry
Database: PDB / ID: 4aw5
TitleComplex of the EphB4 kinase domain with an oxindole inhibitor
ComponentsEPHRIN TYPE-B RECEPTOR 4
KeywordsTRANSFERASE
Function / homology
Function and homology information


ephrin receptor activity / transmembrane-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 ...ephrin receptor activity / transmembrane-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 / axon guidance / receptor protein-tyrosine kinase / angiogenesis / protein autophosphorylation / receptor complex / cell adhesion / dendrite / 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-30K / Ephrin type-B receptor 4
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.33 Å
AuthorsTill, J.H. / Stout, T.J.
CitationJournal: Bioorg.Med.Chem.Lett. / Year: 2012
Title: The Design, Synthesis, and Biological Evaluation of Potent Receptor Tyrosine Kinase Inhibitors.
Authors: Kim, M.H. / Tsuhako, A.L. / Co, E.W. / Aftab, D.T. / Bentzien, F. / Chen, J. / Cheng, W. / Engst, S. / Goon, L. / Klein, R.R. / Le, D.T. / Mac, M. / Parks, J.J. / Qian, F. / Rodriquez, M. / ...Authors: Kim, M.H. / Tsuhako, A.L. / Co, E.W. / Aftab, D.T. / Bentzien, F. / Chen, J. / Cheng, W. / Engst, S. / Goon, L. / Klein, R.R. / Le, D.T. / Mac, M. / Parks, J.J. / Qian, F. / Rodriquez, M. / Stout, T.J. / Till, J.H. / Won, K.A. / Wu, X. / Michael Yakes, F. / Yu, P. / Zhang, W. / Zhao, Y. / Lamb, P. / Nuss, J.M. / Xu, W.
History
DepositionMay 31, 2012Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 1, 2012Provider: repository / Type: Initial release
Revision 1.1May 1, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)33,3902
Polymers32,8971
Non-polymers4941
Water1,63991
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)46.657, 53.978, 63.242
Angle α, β, γ (deg.)90.00, 111.06, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein EPHRIN TYPE-B RECEPTOR 4 / EPHRIN B4 / HEPATOMA TRANSMEMBRANE KINASE / TYROSINE-PROTEIN KINASE TYRO11


Mass: 32896.770 Da / Num. of mol.: 1 / Fragment: KINASE DOMAIN, RESIDUES 605-890
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Cell line (production host): SF9 / Production host: SPODOPTERA FRUGIPERDA (fall armyworm)
References: UniProt: P54760, receptor protein-tyrosine kinase
#2: Chemical ChemComp-30K / (3Z)-5-[(1-ethylpiperidin-4-yl)amino]-3-[(5-methoxy-1H-benzimidazol-2-yl)(phenyl)methylidene]-1,3-dihydro-2H-indol-2-one


Mass: 493.599 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C30H31N5O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 91 / 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: 2.42 Å3/Da / Density % sol: 48.8 % / Description: NONE
Crystal growpH: 8 / Details: pH 8.0

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Data collection

DiffractionMean temperature: 93.2 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 32-ID / Wavelength: 1.00036
DetectorType: MARRESEARCH / Detector: CCD / Date: Oct 25, 2002
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.00036 Å / Relative weight: 1
ReflectionResolution: 2.33→54 Å / Num. obs: 12716 / % possible obs: 100 % / Observed criterion σ(I): -3 / Redundancy: 3.7 % / Rmerge(I) obs: 0.12 / Net I/σ(I): 11.4
Reflection shellResolution: 2.33→2.46 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.46 / Mean I/σ(I) obs: 1.8 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.1.24refinement
MOSFLMdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: IN-HOUSE APO STRUCTURE

Resolution: 2.33→58.72 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.889 / SU B: 8.957 / SU ML: 0.208 / Cross valid method: THROUGHOUT / ESU R: 0.369 / ESU R Free: 0.282 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.27894 642 5.1 %RANDOM
Rwork0.19015 ---
obs0.19439 12054 99.93 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 49.445 Å2
Baniso -1Baniso -2Baniso -3
1-4.05 Å20 Å23.63 Å2
2---3.27 Å20 Å2
3---1.83 Å2
Refinement stepCycle: LAST / Resolution: 2.33→58.72 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2049 0 37 91 2177
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.0222149
X-RAY DIFFRACTIONr_bond_other_d0.0020.021975
X-RAY DIFFRACTIONr_angle_refined_deg1.9381.9732911
X-RAY DIFFRACTIONr_angle_other_deg1.45234582
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.8985261
X-RAY DIFFRACTIONr_dihedral_angle_2_deg
X-RAY DIFFRACTIONr_dihedral_angle_3_deg
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0990.2313
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.022384
X-RAY DIFFRACTIONr_gen_planes_other0.0040.02455
X-RAY DIFFRACTIONr_nbd_refined0.2260.2443
X-RAY DIFFRACTIONr_nbd_other0.2410.22111
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other0.1070.21105
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2070.264
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1190.27
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2720.228
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1130.26
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.9211.51302
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.69422104
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.9943847
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it3.4984.5806
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.33→2.391 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.317 57
Rwork0.261 866

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