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- PDB-5mja: Kinase domain of human EphB1 bound to a quinazoline-based inhibitor -

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Basic information

Entry
Database: PDB / ID: 5mja
TitleKinase domain of human EphB1 bound to a quinazoline-based inhibitor
ComponentsEphrin type-B receptor 1
KeywordsTRANSFERASE / Receptor tyrosine kinase / kinase domain / Inhibitor
Function / homology
Function and homology information


skeletal muscle satellite cell activation / negative regulation of satellite cell differentiation / hindbrain tangential cell migration / negative regulation of skeletal muscle satellite cell proliferation / optic nerve morphogenesis / axon guidance receptor activity / central nervous system projection neuron axonogenesis / immunological synapse formation / filopodium tip / dendritic spine development ...skeletal muscle satellite cell activation / negative regulation of satellite cell differentiation / hindbrain tangential cell migration / negative regulation of skeletal muscle satellite cell proliferation / optic nerve morphogenesis / axon guidance receptor activity / central nervous system projection neuron axonogenesis / immunological synapse formation / filopodium tip / dendritic spine development / camera-type eye morphogenesis / transmembrane-ephrin receptor activity / dendritic spine morphogenesis / neural precursor cell proliferation / positive regulation of synapse assembly / EPH-Ephrin signaling / Ephrin signaling / retinal ganglion cell axon guidance / establishment of cell polarity / cell-substrate adhesion / detection of temperature stimulus involved in sensory perception of pain / regulation of JNK cascade / EPH-ephrin mediated repulsion of cells / ephrin receptor signaling pathway / EPHB-mediated forward signaling / neurogenesis / regulation of ERK1 and ERK2 cascade / cell chemotaxis / axon guidance / modulation of chemical synaptic transmission / receptor protein-tyrosine kinase / early endosome membrane / angiogenesis / protein autophosphorylation / membrane raft / axon / glutamatergic synapse / dendrite / protein-containing complex binding / endoplasmic reticulum / extracellular exosome / extracellular region / ATP binding / plasma membrane / cytosol
Similarity search - Function
Ephrin type-B receptor 1, ligand binding domain / EphB1 , SAM domain / 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. ...Ephrin type-B receptor 1, ligand binding domain / EphB1 , SAM domain / 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-7O3 / Ephrin type-B receptor 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.14 Å
AuthorsKung, A. / Schimpl, M. / Chen, Y.-C. / Overman, R.C. / Zhang, C.
CitationJournal: ACS Chem. Biol. / Year: 2017
Title: A Chemical-Genetic Approach to Generate Selective Covalent Inhibitors of Protein Kinases.
Authors: Kung, A. / Schimpl, M. / Ekanayake, A. / Chen, Y.C. / Overman, R. / Zhang, C.
History
DepositionNov 30, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 17, 2017Provider: repository / Type: Initial release
Revision 1.1Jun 28, 2017Group: Database references / Category: citation
Item: _citation.country / _citation.journal_volume ..._citation.country / _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Jan 24, 2018Group: Source and taxonomy / Category: entity_src_gen
Item: _entity_src_gen.pdbx_host_org_ncbi_taxonomy_id / _entity_src_gen.pdbx_host_org_scientific_name / _entity_src_gen.pdbx_host_org_strain
Revision 1.3Jan 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

Downloads & links

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Assembly

Deposited unit
A: Ephrin type-B receptor 1
B: Ephrin type-B receptor 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,6346
Polymers69,7152
Non-polymers9194
Water6,125340
1
A: Ephrin type-B receptor 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,3173
Polymers34,8581
Non-polymers4592
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Ephrin type-B receptor 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,3173
Polymers34,8581
Non-polymers4592
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)101.806, 101.806, 157.140
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121

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Components

#1: Protein Ephrin type-B receptor 1 / ELK / EPH tyrosine kinase 2 / EPH-like kinase 6 / hEK6 / Neuronally-expressed EPH-related tyrosine ...ELK / EPH tyrosine kinase 2 / EPH-like kinase 6 / hEK6 / Neuronally-expressed EPH-related tyrosine kinase / NET / Tyrosine-protein kinase receptor EPH-2


Mass: 34857.613 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: phosphorylation on Tyr647 and Tyr778 as a result of autophosphorylation during recombinant expression in E.coli
Source: (gene. exp.) Homo sapiens (human) / Gene: EPHB1, ELK, EPHT2, HEK6, NET / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): GOLD
References: UniProt: P54762, receptor protein-tyrosine kinase
#2: Chemical ChemComp-7O3 / 2-chloranyl-~{N}-[4-[(2-chloranyl-5-oxidanyl-phenyl)amino]quinazolin-7-yl]ethanamide


Mass: 363.198 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C16H12Cl2N4O2
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 340 / 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: 3.39 Å3/Da / Density % sol: 63.71 % / Description: hexagonal plates
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 18 % PEG3350, 0.1-0.2 M ammonium sulfate, 0.1 M PCTP (Sodium propionate, Sodium cacodylate trihydrate, Bis-Tris propane) buffer pH 6-9

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9795 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Jun 18, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.14→76.89 Å / Num. obs: 52668 / % possible obs: 100 % / Redundancy: 19.7 % / Biso Wilson estimate: 46.46 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.108 / Net I/σ(I): 16.2
Reflection shellResolution: 2.14→2.2 Å / Redundancy: 19.3 % / Rmerge(I) obs: 2.164 / Mean I/σ(I) obs: 1.5 / CC1/2: 0.62 / % possible all: 100

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Processing

Software
NameVersionClassification
BUSTER2.11.6refinement
DIALSdata reduction
Aimlessdata scaling
BUSTER2.11.6phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3ZFX chain A

3zfx


Resolution: 2.14→76.89 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.926 / Rfactor Rfree error: 0 / SU R Cruickshank DPI: 0.162 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.168 / SU Rfree Blow DPI: 0.155 / SU Rfree Cruickshank DPI: 0.152
RfactorNum. reflection% reflectionSelection details
Rfree0.236 2569 4.9 %RANDOM
Rwork0.2 ---
obs0.202 52480 99.7 %-
Displacement parametersBiso mean: 52.05 Å2
Baniso -1Baniso -2Baniso -3
1-1.0853 Å20 Å20 Å2
2--1.0853 Å20 Å2
3----2.1706 Å2
Refine analyzeLuzzati coordinate error obs: 0.29 Å
Refinement stepCycle: 1 / Resolution: 2.14→76.89 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4322 0 122 340 4784
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.014537HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.056135HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d1580SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes105HARMONIC2
X-RAY DIFFRACTIONt_gen_planes651HARMONIC5
X-RAY DIFFRACTIONt_it4537HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion3.45
X-RAY DIFFRACTIONt_other_torsion16.96
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion569SEMIHARMONIC5
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_contact5513SEMIHARMONIC4
LS refinement shellResolution: 2.14→2.2 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.319 183 4.81 %
Rwork0.283 3624 -
all0.285 3807 -
obs--99.15 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.84980.22160.21391.7837-0.06871.9192-0.0983-0.0787-0.10390.12370.1327-0.420.06770.169-0.0344-0.19780.02360.0024-0.20180.0006-0.0578-2.125639.7153-2.9347
22.1980.54470.6061.23360.16651.2283-0.05750.01820.10690.10130.08180.2543-0.064-0.1944-0.0243-0.17070.02020.0487-0.0930.0895-0.09-33.40440.1416-6.121
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1{ A|* }
2X-RAY DIFFRACTION2{ B|* }

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