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- PDB-5d12: Kinase domain of cSrc in complex with RL40 -

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Basic information

Entry
Database: PDB / ID: 5d12
TitleKinase domain of cSrc in complex with RL40
ComponentsProto-oncogene tyrosine-protein kinase Src
KeywordsTRANSFERASE / kinase inhibitor / drug resistance
Function / homology
Function and homology information


Signaling by ERBB2 / Nuclear signaling by ERBB4 / Signaling by SCF-KIT / Regulation of KIT signaling / Signaling by EGFR / GAB1 signalosome / Regulation of gap junction activity / FCGR activation / PECAM1 interactions / Co-stimulation by CD28 ...Signaling by ERBB2 / Nuclear signaling by ERBB4 / Signaling by SCF-KIT / Regulation of KIT signaling / Signaling by EGFR / GAB1 signalosome / Regulation of gap junction activity / FCGR activation / PECAM1 interactions / Co-stimulation by CD28 / Co-inhibition by CTLA4 / EPHA-mediated growth cone collapse / Ephrin signaling / G alpha (i) signalling events / GP1b-IX-V activation signalling / Thrombin signalling through proteinase activated receptors (PARs) / VEGFR2 mediated cell proliferation / RET signaling / Receptor Mediated Mitophagy / ADP signalling through P2Y purinoceptor 1 / RAF activation / PIP3 activates AKT signaling / EPH-ephrin mediated repulsion of cells / PI5P, PP2A and IER3 Regulate PI3K/AKT Signaling / Activated NTRK3 signals through PI3K / Downstream signal transduction / Downregulation of ERBB4 signaling / Cyclin D associated events in G1 / Regulation of RUNX3 expression and activity / MAP2K and MAPK activation / 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 / connexin binding / negative regulation of intrinsic apoptotic signaling pathway / immune system process / progesterone receptor signaling pathway / negative regulation of extrinsic apoptotic signaling pathway / non-membrane spanning protein tyrosine kinase activity / non-specific protein-tyrosine kinase / epidermal growth factor receptor signaling pathway / cell junction / cell-cell junction / protein tyrosine kinase activity / protein phosphatase binding / cell differentiation / cytoskeleton / mitochondrial inner membrane / regulation of cell cycle / cell adhesion / endosome membrane / signaling receptor binding / focal adhesion / heme binding / perinuclear region of cytoplasm / protein-containing complex / ATP binding / nucleus / membrane / plasma membrane / cytosol
Similarity search - Function
: / SH3 domain / SH2 domain / Src homology 2 (SH2) domain profile. / Src homology 2 domains / SH2 domain / SH2 domain superfamily / Src homology 3 domains / SH3-like domain superfamily / Src homology 3 (SH3) domain profile. ...: / SH3 domain / SH2 domain / Src homology 2 (SH2) domain profile. / Src homology 2 domains / SH2 domain / SH2 domain superfamily / Src homology 3 domains / SH3-like domain superfamily / Src homology 3 (SH3) domain profile. / SH3 domain / Tyrosine-protein kinase, catalytic domain / Tyrosine kinase, catalytic domain / Tyrosine protein kinases specific active-site signature. / Tyrosine-protein kinase, active site / Serine-threonine/tyrosine-protein kinase, catalytic domain / Protein tyrosine and serine/threonine kinase / 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-G97 / Proto-oncogene tyrosine-protein kinase Src
Similarity search - Component
Biological speciesGallus gallus (chicken)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 3 Å
AuthorsBecker, C. / Richters, A. / Engel, J. / Rauh, D.
CitationJournal: J.Med.Chem. / Year: 2015
Title: Targeting Drug Resistance in EGFR with Covalent Inhibitors: A Structure-Based Design Approach.
Authors: Engel, J. / Richters, A. / Getlik, M. / Tomassi, S. / Keul, M. / Termathe, M. / Lategahn, J. / Becker, C. / Mayer-Wrangowski, S. / Grutter, C. / Uhlenbrock, N. / Krull, J. / Schaumann, N. / ...Authors: Engel, J. / Richters, A. / Getlik, M. / Tomassi, S. / Keul, M. / Termathe, M. / Lategahn, J. / Becker, C. / Mayer-Wrangowski, S. / Grutter, C. / Uhlenbrock, N. / Krull, J. / Schaumann, N. / Eppmann, S. / Kibies, P. / Hoffgaard, F. / Heil, J. / Menninger, S. / Ortiz-Cuaran, S. / Heuckmann, J.M. / Tinnefeld, V. / Zahedi, R.P. / Sos, M.L. / Schultz-Fademrecht, C. / Thomas, R.K. / Kast, S.M. / Rauh, D.
History
DepositionAug 3, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Sep 9, 2015Provider: repository / Type: Initial release
Revision 1.1Sep 23, 2015Group: Database references
Revision 1.2Feb 20, 2019Group: Advisory / Data collection / Derived calculations
Category: pdbx_data_processing_status / pdbx_validate_close_contact ...pdbx_data_processing_status / pdbx_validate_close_contact / struct_conn / struct_conn_type
Revision 1.3May 8, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
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: Proto-oncogene tyrosine-protein kinase Src
B: Proto-oncogene tyrosine-protein kinase Src
hetero molecules


Theoretical massNumber of molelcules
Total (without water)66,2584
Polymers65,5462
Non-polymers7132
Water00
1
A: Proto-oncogene tyrosine-protein kinase Src
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,1292
Polymers32,7731
Non-polymers3561
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Proto-oncogene tyrosine-protein kinase Src
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,1292
Polymers32,7731
Non-polymers3561
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)42.270, 63.790, 74.970
Angle α, β, γ (deg.)101.56, 89.91, 89.98
Int Tables number1
Space group name H-MP1

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Components

#1: Protein Proto-oncogene tyrosine-protein kinase Src / Proto-oncogene c-Src / pp60c-src / p60-Src


Mass: 32772.801 Da / Num. of mol.: 2 / Fragment: UNP residues 251-533 / Mutation: T338M, S345C
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Gallus gallus (chicken) / Gene: SRC / Production host: Escherichia coli (E. coli)
References: UniProt: P00523, non-specific protein-tyrosine kinase
#2: Chemical ChemComp-G97 / N-[2-phenyl-4-(1H-pyrazol-3-ylamino)quinazolin-7-yl]prop-2-enamide / Proto-oncogene c-Src / pp60c-src / p60-Src / N-(4-(1H-pyrazol-3-ylamino)-2-phenylquinazolin-7-yl)acrylamide


Mass: 356.381 Da / Num. of mol.: 2 / Fragment: UNP residues 251-533 / Mutation: T338M, S345C
Source method: isolated from a genetically manipulated source
Formula: C20H16N6O / Source: (gene. exp.) Gallus gallus (chicken) / Gene: SRC / Production host: Escherichia coli (E. coli) / References: non-specific protein-tyrosine kinase

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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: 3.02 Å3/Da / Density % sol: 59.29 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: 0.085-0.125 mM MES, 9-11.5 % PEG20000 / PH range: pH 6.0 - 7.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1.0039 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: May 26, 2010
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0039 Å / Relative weight: 1
ReflectionResolution: 3→45 Å / Num. obs: 14548 / % possible obs: 94.6 % / Observed criterion σ(I): -3 / Redundancy: 3.09 % / Biso Wilson estimate: 34.039 Å2 / Rmerge F obs: 0.267 / Rmerge(I) obs: 0.19 / Rrim(I) all: 0.231 / Χ2: 0.89 / Net I/σ(I): 9.39 / Num. measured all: 44960
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Highest resolution (Å)Rmerge F obsRmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsRrim(I) all% possible all
3-3.10.5790.54.244286140913500.695.8
3.1-3.20.5380.4744.944111133612890.56996.5
3.2-3.30.4830.4195.773329107010390.50397.1
3.3-3.60.3460.277.227848267025480.32895.4
3.6-4.40.2280.17810.0111391401337510.21893.5
4.4-6.20.2230.17711.868939314429440.21893.6
6.2-80.1090.09714.828089208820.11795.9
8-120.0680.05518.2115105755170.06989.9
12-160.050.04822.534461401340.05995.7
160.040.03623.18292103940.04591.3

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Processing

Software
NameVersionClassification
REFMAC5.8.0073refinement
XSCALEdata scaling
PDB_EXTRACT3.15data extraction
RefinementResolution: 3→43.49 Å / Cor.coef. Fo:Fc: 0.827 / Cor.coef. Fo:Fc free: 0.725 / SU B: 30.366 / SU ML: 0.589 / Cross valid method: THROUGHOUT / ESU R Free: 0.642 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.37648 728 5 %RANDOM
Rwork0.28986 ---
obs0.29417 13820 94.66 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 33.119 Å2
Baniso -1Baniso -2Baniso -3
1--0.01 Å2-0.63 Å21.05 Å2
2---3.27 Å2-0.4 Å2
3---3.18 Å2
Refinement stepCycle: LAST / Resolution: 3→43.49 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4140 0 0 0 4140
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0194264
X-RAY DIFFRACTIONr_bond_other_d0.0070.024018
X-RAY DIFFRACTIONr_angle_refined_deg1.981.9855780
X-RAY DIFFRACTIONr_angle_other_deg1.06639236
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.5155513
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.44823.717191
X-RAY DIFFRACTIONr_dihedral_angle_3_deg26.51115724
X-RAY DIFFRACTIONr_dihedral_angle_4_deg23.2011530
X-RAY DIFFRACTIONr_chiral_restr0.1030.2617
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0214763
X-RAY DIFFRACTIONr_gen_planes_other0.0030.02991
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_it1.6053.3892052
X-RAY DIFFRACTIONr_mcbond_other1.6023.3892051
X-RAY DIFFRACTIONr_mcangle_it2.7965.0742556
X-RAY DIFFRACTIONr_mcangle_other2.7965.0742557
X-RAY DIFFRACTIONr_scbond_it1.1973.3732212
X-RAY DIFFRACTIONr_scbond_other1.1963.3722213
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.1215.0373222
X-RAY DIFFRACTIONr_long_range_B_refined4.65427.1855402
X-RAY DIFFRACTIONr_long_range_B_other4.65327.1825403
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 3→3.078 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.47 56 -
Rwork0.329 1051 -
obs--96.26 %

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