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- PDB-2xvd: ephB4 kinase domain inhibitor complex -

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Basic information

Entry
Database: PDB / ID: 2xvd
TitleephB4 kinase domain inhibitor complex
ComponentsEPHRIN TYPE-B RECEPTOR 4
KeywordsTRANSFERASE / NUCLEOTIDE-BINDING
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-AS6 / Ephrin type-B receptor 4
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsRead, J. / Brassington, C.A. / Green, I. / McCall, E.J. / Valentine, A.L.
CitationJournal: Bioorg.Med.Chem.Lett. / Year: 2011
Title: Inhibitors of the Tyrosine Kinase Ephb4. Part 4: Discovery and Optimization of a Benzylic Alcohol Series.
Authors: Barlaam, B. / Ducray, R. / Lambert-Van Der Brempt, C. / Ple, P. / Bardelle, C. / Brooks, N. / Coleman, T. / Cross, D. / Kettle, J.G. / Read, J.
History
DepositionOct 25, 2010Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 8, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Jun 28, 2017Group: 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
Revision 1.4Dec 20, 2023Group: 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 / pdbx_struct_conn_angle / struct_conn / 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 / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _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)34,5195
Polymers33,9351
Non-polymers5854
Water3,909217
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)46.708, 53.315, 61.330
Angle α, β, γ (deg.)90.00, 111.75, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein EPHRIN TYPE-B RECEPTOR 4 / TYROSINE-PROTEIN KINASE TYRO11 / TYROSINE-PROTEIN KINASE RECEPTOR HTK


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-AS6 / {4-METHYL-3-[(1-METHYLETHYL)(2-{[3-(METHYLSULFONYL)-5-MORPHOLIN-4-YLPHENYL]AMINO}PYRIMIDIN-4-YL)AMINO]PHENYL}METHANOL


Mass: 511.636 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C26H33N5O4S
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mg
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 217 / Source method: isolated from a natural source / Formula: H2O
Compound detailsENGINEERED RESIDUE IN CHAIN A, TYR 774 TO GLU
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: 2.09 Å3/Da / Density % sol: 41.15 % / Description: NONE
Crystal growpH: 7.5 / Details: PH 7.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 / Wavelength: 1.5418
DetectorType: RIGAKU CCD / Detector: CCD / Date: Sep 13, 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: 1.7→43 Å / Num. obs: 28154 / % possible obs: 90.9 % / Observed criterion σ(I): 2 / Redundancy: 3.32 % / Biso Wilson estimate: 23.9 Å2 / Rmerge(I) obs: 0.05 / Net I/σ(I): 14.3
Reflection shellResolution: 1.7→1.76 Å / Redundancy: 2.06 % / Rmerge(I) obs: 0.36 / Mean I/σ(I) obs: 2 / % possible all: 46.9

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Processing

Software
NameVersionClassification
REFMAC5.5.0109refinement
d*TREKdata reduction
d*TREKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2VWU

2vwu


Resolution: 1.7→43.05 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.951 / SU B: 5.367 / SU ML: 0.078 / Cross valid method: THROUGHOUT / ESU R: 0.114 / ESU R Free: 0.11 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.20913 1414 5 %RANDOM
Rwork0.1751 ---
obs0.17687 26740 90.91 %-
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: 30.912 Å2
Baniso -1Baniso -2Baniso -3
1--0.3 Å20 Å2-0.44 Å2
2---0.41 Å20 Å2
3---0.38 Å2
Refinement stepCycle: LAST / Resolution: 1.7→43.05 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2072 0 39 217 2328
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0222160
X-RAY DIFFRACTIONr_bond_other_d0.0010.021437
X-RAY DIFFRACTIONr_angle_refined_deg1.4361.9782933
X-RAY DIFFRACTIONr_angle_other_deg0.94533492
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.6815269
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.67923.55690
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.25915350
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.6471516
X-RAY DIFFRACTIONr_chiral_restr0.0910.2323
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0212440
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02433
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.7921.51350
X-RAY DIFFRACTIONr_mcbond_other0.1931.5544
X-RAY DIFFRACTIONr_mcangle_it1.43922169
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.113810
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it3.3654.5764
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: 1.7→1.744 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.281 51 -
Rwork0.288 940 -
obs--43.66 %
Refinement TLS params.Method: refined / Origin x: 10.2452 Å / Origin y: -0.0932 Å / Origin z: 1.3566 Å
111213212223313233
T0.0007 Å2-0.0008 Å2-0.0003 Å2-0.0125 Å2-0.0051 Å2--0.0222 Å2
L0.821 °2-0.1488 °20.0444 °2-0.7379 °2-0.0312 °2--0.9923 °2
S-0.001 Å °-0.027 Å °-0.0036 Å °0.0208 Å °-0.0068 Å °0.0258 Å °0.0062 Å °-0.104 Å °0.0078 Å °

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