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- PDB-6jmf: Crystal structure of human tyrosine-protein kinase Fes/Fps in com... -

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Basic information

Entry
Database: PDB / ID: 6jmf
TitleCrystal structure of human tyrosine-protein kinase Fes/Fps in complex with compound 4
ComponentsTyrosine-protein kinase Fes/Fps
KeywordsTRANSFERASE / FES / c-Fes / tyrosine protein kinase
Function / homology
Function and homology information


positive regulation of myeloid cell differentiation / regulation of mast cell degranulation / regulation of vesicle-mediated transport / cellular response to vitamin D / SEMA3A-Plexin repulsion signaling by inhibiting Integrin adhesion / CRMPs in Sema3A signaling / microtubule bundle formation / positive regulation of monocyte differentiation / regulation of cell motility / centrosome cycle ...positive regulation of myeloid cell differentiation / regulation of mast cell degranulation / regulation of vesicle-mediated transport / cellular response to vitamin D / SEMA3A-Plexin repulsion signaling by inhibiting Integrin adhesion / CRMPs in Sema3A signaling / microtubule bundle formation / positive regulation of monocyte differentiation / regulation of cell motility / centrosome cycle / myoblast proliferation / cardiac muscle cell proliferation / regulation of cell differentiation / Sema3A PAK dependent Axon repulsion / regulation of cell adhesion / positive regulation of microtubule polymerization / immunoglobulin receptor binding / phosphatidylinositol binding / non-specific protein-tyrosine kinase / non-membrane spanning protein tyrosine kinase activity / Signaling by SCF-KIT / cytoplasmic side of plasma membrane / positive regulation of neuron projection development / peptidyl-tyrosine phosphorylation / chemotaxis / microtubule cytoskeleton / regulation of cell population proliferation / regulation of cell shape / cytoplasmic vesicle / microtubule binding / protein tyrosine kinase activity / protein autophosphorylation / cell adhesion / focal adhesion / Golgi apparatus / ATP binding / cytoplasm / cytosol
Similarity search - Function
Tyrosine-protein kinase, Fes/Fps type / Fes/Fps/Fer, SH2 domain / Fes/CIP4, and EFC/F-BAR homology domain / Fes/CIP4 homology domain / FCH domain / F-BAR domain / F-BAR domain profile. / AH/BAR domain superfamily / SH2 domain / Src homology 2 (SH2) domain profile. ...Tyrosine-protein kinase, Fes/Fps type / Fes/Fps/Fer, SH2 domain / Fes/CIP4, and EFC/F-BAR homology domain / Fes/CIP4 homology domain / FCH domain / F-BAR domain / F-BAR domain profile. / AH/BAR domain superfamily / SH2 domain / Src homology 2 (SH2) domain profile. / Src homology 2 domains / SH2 domain / SH2 domain 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 / Protein kinase, ATP binding site / Protein kinases ATP-binding region signature. / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily
Similarity search - Domain/homology
Chem-9FC / Tyrosine-protein kinase Fes/Fps
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsBaba, D. / Hanzawa, H.
CitationJournal: Acs Med.Chem.Lett. / Year: 2019
Title: Discovery of Novel Pyrido-pyridazinone Derivatives as FER Tyrosine Kinase Inhibitors with Antitumor Activity.
Authors: Taniguchi, T. / Inagaki, H. / Baba, D. / Yasumatsu, I. / Toyota, A. / Kaneta, Y. / Kiga, M. / Iimura, S. / Odagiri, T. / Shibata, Y. / Ueda, K. / Seo, M. / Shimizu, H. / Imaoka, T. / Nakayama, K.
History
DepositionMar 8, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 12, 2019Provider: repository / Type: Initial release
Revision 1.1Nov 22, 2023Group: 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: Tyrosine-protein kinase Fes/Fps
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,0404
Polymers42,4841
Non-polymers5573
Water2,846158
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area240 Å2
ΔGint-21 kcal/mol
Surface area18210 Å2
MethodPISA
Unit cell
Length a, b, c (Å)80.790, 80.790, 131.668
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number173
Space group name H-MP63

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Components

#1: Protein Tyrosine-protein kinase Fes/Fps / Feline sarcoma/Fujinami avian sarcoma oncogene homolog / Proto-oncogene c-Fes / Proto-oncogene c- ...Feline sarcoma/Fujinami avian sarcoma oncogene homolog / Proto-oncogene c-Fes / Proto-oncogene c-Fps / p93c-fes


Mass: 42483.668 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: FES, FPS / Production host: Escherichia coli (E. coli)
References: UniProt: P07332, non-specific protein-tyrosine kinase
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-9FC / 6-{[(1R,2S)-2-aminocyclohexyl]amino}-5-cyano-2-[(3-methylphenyl)amino]pyridine-3-carboxamide


Mass: 364.444 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C20H24N6O / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 158 / 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: 2.68 Å3/Da / Density % sol: 54.03 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 0.1 M BisTrisPropane, 0.2 M Sodium Salfate, 15% PEG 3350, 10% Ethylene glycol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-1A / Wavelength: 1.1 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Jan 29, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. obs: 32995 / % possible obs: 99.8 % / Redundancy: 6.7 % / Net I/σ(I): 24.88
Reflection shellResolution: 2→2.07 Å

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Processing

Software
NameVersionClassification
REFMAC5.6.0117refinement
HKL-2000data reduction
SCALEPACKdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3BKB

3bkb


Resolution: 2→30 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.923 / SU B: 3.617 / SU ML: 0.103 / Cross valid method: THROUGHOUT / ESU R: 0.166 / ESU R Free: 0.156
RfactorNum. reflection% reflectionSelection details
Rfree0.24082 1596 4.9 %RANDOM
Rwork0.19737 ---
obs0.19938 31069 99.34 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å
Displacement parametersBiso mean: 26.576 Å2
Baniso -1Baniso -2Baniso -3
1--0.02 Å2-0.01 Å20 Å2
2---0.02 Å20 Å2
3---0.03 Å2
Refinement stepCycle: 1 / Resolution: 2→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2945 0 37 158 3140
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0193051
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.2271.9794137
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.415371
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.80323.358137
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.10515519
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.9491524
X-RAY DIFFRACTIONr_chiral_restr0.0770.2450
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0212340
X-RAY DIFFRACTIONr_gen_planes_other
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_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
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→2.052 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.268 135 -
Rwork0.223 2124 -
obs--94.28 %

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