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- PDB-2jkq: Focal Adhesion Kinase catalytic domain in complex with bis-anilin... -

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Basic information

Entry
Database: PDB / ID: 2jkq
TitleFocal Adhesion Kinase catalytic domain in complex with bis-anilino pyrimidine inhibitor
ComponentsFOCAL ADHESION KINASE 1
KeywordsTRANSFERASE / NUCLEOTIDE-BINDING / TYROSINE-PROTEIN KINASE / KINASE INHIBITOR / INTEGRIN SIGNALING / KINASE / ATP-BINDING / CELL MIGRATION / FOCAL ADHESION
Function / homology
Function and homology information


Apoptotic cleavage of cellular proteins / NCAM signaling for neurite out-growth / RAF/MAP kinase cascade / Turbulent (oscillatory, disturbed) flow shear stress activates signaling by PIEZO1 and integrins in endothelial cells / RHO GTPases Activate WASPs and WAVEs / Regulation of actin dynamics for phagocytic cup formation / negative regulation of protein autophosphorylation / radial glia-guided pyramidal neuron migration / calcium-dependent cysteine-type endopeptidase activity / positive regulation of substrate-dependent cell migration, cell attachment to substrate ...Apoptotic cleavage of cellular proteins / NCAM signaling for neurite out-growth / RAF/MAP kinase cascade / Turbulent (oscillatory, disturbed) flow shear stress activates signaling by PIEZO1 and integrins in endothelial cells / RHO GTPases Activate WASPs and WAVEs / Regulation of actin dynamics for phagocytic cup formation / negative regulation of protein autophosphorylation / radial glia-guided pyramidal neuron migration / calcium-dependent cysteine-type endopeptidase activity / positive regulation of substrate-dependent cell migration, cell attachment to substrate / Integrin signaling / GRB2:SOS provides linkage to MAPK signaling for Integrins / DCC mediated attractive signaling / MET activates PTK2 signaling / Extra-nuclear estrogen signaling / EPHB-mediated forward signaling / p130Cas linkage to MAPK signaling for integrins / VEGFA-VEGFR2 Pathway / signal complex assembly / response to pH / angiogenesis involved in wound healing / wound healing, spreading of cells / positive regulation of protein tyrosine kinase activity / negative regulation of anoikis / negative regulation of cell-substrate adhesion / positive regulation of focal adhesion assembly / positive regulation of protein binding / regulation of cell adhesion / response to muscle stretch / molecular function activator activity / actin filament organization / non-membrane spanning protein tyrosine kinase activity / non-specific protein-tyrosine kinase / sarcolemma / integrin binding / epidermal growth factor receptor signaling pathway / protein autophosphorylation / protease binding / protein tyrosine kinase activity / cell cortex / positive regulation of cell migration / ciliary basal body / focal adhesion / positive regulation of cell population proliferation / centrosome / perinuclear region of cytoplasm / ATP binding / identical protein binding / nucleus / plasma membrane / cytoplasm
Similarity search - Function
Focal adhesion kinase, targeting (FAT) domain / Focal adhesion kinase, targeting (FAT) domain superfamily / Focal adhesion kinase, N-terminal / FAK1/PYK2, FERM domain C-lobe / Focal adhesion targeting region / FERM N-terminal domain / : / FAK1/PYK2, FERM domain C-lobe / FERM domain signature 2. / FERM central domain ...Focal adhesion kinase, targeting (FAT) domain / Focal adhesion kinase, targeting (FAT) domain superfamily / Focal adhesion kinase, N-terminal / FAK1/PYK2, FERM domain C-lobe / Focal adhesion targeting region / FERM N-terminal domain / : / FAK1/PYK2, FERM domain C-lobe / FERM domain signature 2. / FERM central domain / FERM/acyl-CoA-binding protein superfamily / FERM central domain / FERM superfamily, second domain / FERM domain / FERM domain profile. / Band 4.1 domain / Band 4.1 homologues / Tyrosine-protein kinase, catalytic domain / Tyrosine kinase, catalytic domain / Tyrosine protein kinases specific active-site signature. / PH-like domain superfamily / Tyrosine-protein kinase, active site / Serine-threonine/tyrosine-protein kinase, catalytic domain / Protein tyrosine and serine/threonine kinase / Ubiquitin-like domain superfamily / 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. / 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-VG8 / Focal adhesion kinase 1
Similarity search - Component
Biological speciesGALLUS GALLUS (chicken)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsLietha, D. / Eck, M.J.
CitationJournal: Plos One / Year: 2008
Title: Crystal Structures of the Fak Kinase in Complex with Tae226 and Related Bis-Anilino Pyrimidine Inhibitors Reveal a Helical Dfg Conformation.
Authors: Lietha, D. / Eck, M.J.
History
DepositionAug 29, 2008Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 9, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Apr 3, 2019Group: Data collection / Other / Source and taxonomy
Category: entity_src_gen / pdbx_database_proc / pdbx_database_status
Item: _entity_src_gen.pdbx_host_org_cell_line / _pdbx_database_status.recvd_author_approval
Revision 1.3Dec 13, 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 / 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
Revision 1.4Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: FOCAL ADHESION KINASE 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,3212
Polymers31,7591
Non-polymers5621
Water43224
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)44.523, 44.887, 66.435
Angle α, β, γ (deg.)90.00, 95.42, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein FOCAL ADHESION KINASE 1 / FOCAL ADHESION KINASE / FADK 1


Mass: 31758.762 Da / Num. of mol.: 1 / Fragment: KINASE DOMAIN, RESIDUES 411-686
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) GALLUS GALLUS (chicken) / Plasmid: PACG2T / Cell line (production host): High Five / Production host: TRICHOPLUSIA NI (cabbage looper)
References: UniProt: Q00944, non-specific protein-tyrosine kinase
#2: Chemical ChemComp-VG8 / 4-(1,4'-bipiperidin-1'-yl)-7-({5-chloro-2-[(2-methoxyphenyl)amino]pyrimidin-4-yl}amino)-2-methyl-2,3-dihydro-1H-isoindol-1-one


Mass: 562.106 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C30H36ClN7O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 24 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.06 Å3/Da / Density % sol: 40.4 % / Description: NONE
Crystal growpH: 8.5 / Details: 31% PEG4000, 0.1 M TRIS PH 8.5, 10 MM TCEP

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 1.1
DetectorType: ADSC CCD / Detector: CCD / Date: Mar 3, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 2.6→50 Å / Num. obs: 7576 / % possible obs: 92.1 % / Observed criterion σ(I): 0 / Redundancy: 4.2 % / Rmerge(I) obs: 0.18 / Net I/σ(I): 8
Reflection shellResolution: 2.6→2.69 Å / Redundancy: 3 % / Rmerge(I) obs: 0.29 / Mean I/σ(I) obs: 3.08 / % possible all: 63.4

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
HKL-2000data reduction
SCALEPACKdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1MP8

1mp8


Resolution: 2.6→33.08 Å / Cor.coef. Fo:Fc: 0.924 / Cor.coef. Fo:Fc free: 0.872 / SU B: 29.494 / SU ML: 0.308 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R Free: 0.386 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.26187 339 4.5 %RANDOM
Rwork0.21504 ---
obs0.217 7222 92.07 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 33.624 Å2
Baniso -1Baniso -2Baniso -3
1-0.2 Å20 Å2-1.19 Å2
2--0.07 Å20 Å2
3----0.49 Å2
Refinement stepCycle: LAST / Resolution: 2.6→33.08 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2064 0 40 24 2128
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0222156
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.2951.9872920
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.545256
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.36123.36895
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.51615377
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.4091517
X-RAY DIFFRACTIONr_chiral_restr0.0850.2317
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.021619
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2080.2948
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3080.21480
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1740.266
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.240.246
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1650.22
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.5791.51339
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.6122086
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.1523955
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it1.7434.5834
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: 2.601→2.668 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.448 12
Rwork0.268 356
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)
13.14-0.9005-0.97743.59951.67697.25930.17730.05660.35090.2581-0.0464-0.0087-0.40210.4842-0.13080.04820.0170.2355-0.08140.03680.17375.86713.50128.463
23.7235-0.119-1.7213.84410.00283.5398-0.01330.1645-0.1066-0.1994-0.0064-0.1908-0.035-0.04550.0197-0.12660.02250.1555-0.0602-0.03910.033312.643-5.35710.014
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A414 - 503
2X-RAY DIFFRACTION2A504 - 686

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