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- PDB-3tz7: Kinase domain of cSrc in complex with RL103 -

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Basic information

Entry
Database: PDB / ID: 3tz7
TitleKinase domain of cSrc in complex with RL103
ComponentsProto-oncogene tyrosine-protein kinase Src
KeywordsTRANSFERASE/TRANSFERASE INHIBITOR / Type II / Allosteric / DFG-out / Drug resistance mutations / Tyrosin-protein kinase / TRANSFERASE-TRANSFERASE INHIBITOR complex
Function / homology
Function and homology information


Signaling by ERBB2 / Nuclear signaling by ERBB4 / PIP3 activates AKT signaling / Signaling by SCF-KIT / Regulation of KIT signaling / Signaling by EGFR / GAB1 signalosome / Regulation of gap junction activity / FCGR activation / PECAM1 interactions ...Signaling by ERBB2 / Nuclear signaling by ERBB4 / PIP3 activates AKT signaling / Signaling by SCF-KIT / Regulation of KIT signaling / Signaling by EGFR / GAB1 signalosome / Regulation of gap junction activity / FCGR activation / PECAM1 interactions / CD28 co-stimulation / CTLA4 inhibitory signaling / EPHA-mediated growth cone collapse / Ephrin signaling / G alpha (i) signalling events / GP1b-IX-V activation signalling / Recycling pathway of L1 / Thrombin signalling through proteinase activated receptors (PARs) / VEGFR2 mediated cell proliferation / RAF activation / PI5P, PP2A and IER3 Regulate PI3K/AKT Signaling / RET signaling / Receptor Mediated Mitophagy / ADP signalling through P2Y purinoceptor 1 / Downregulation of ERBB4 signaling / EPH-ephrin mediated repulsion of cells / Cyclin D associated events in G1 / Regulation of RUNX3 expression and activity / Activated NTRK3 signals through PI3K / Downstream signal transduction / MAP2K and MAPK activation / Integrin signaling / GRB2:SOS provides linkage to MAPK signaling for Integrins / MET activates PTK2 signaling / Extra-nuclear estrogen signaling / EPHB-mediated forward signaling / p130Cas linkage to MAPK signaling for integrins / VEGFA-VEGFR2 Pathway / connexin binding / osteoclast development / progesterone receptor signaling pathway / negative regulation of intrinsic apoptotic signaling pathway / bone resorption / extrinsic component of cytoplasmic side of plasma membrane / negative regulation of extrinsic apoptotic signaling pathway / non-specific protein-tyrosine kinase / non-membrane spanning protein tyrosine kinase activity / epidermal growth factor receptor signaling pathway / cell junction / protein phosphatase binding / protein tyrosine kinase activity / mitochondrial inner membrane / cell differentiation / cytoskeleton / endosome membrane / regulation of cell cycle / cell adhesion / cell cycle / phosphorylation / signaling receptor binding / focal adhesion / innate immune response / heme binding / perinuclear region of cytoplasm / protein-containing complex / ATP binding / membrane / nucleus / plasma membrane / cytosol
Similarity search - Function
SH3 domain / SH2 domain / Src homology 2 (SH2) domain profile. / Src homology 2 domains / Src homology 3 domains / SH2 domain / SH2 domain superfamily / SH3-like domain superfamily / Src homology 3 (SH3) domain profile. / SH3 domain ...SH3 domain / SH2 domain / Src homology 2 (SH2) domain profile. / Src homology 2 domains / Src homology 3 domains / SH2 domain / SH2 domain superfamily / 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 / 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. / 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-AQB / Proto-oncogene tyrosine-protein kinase Src
Similarity search - Component
Biological speciesGallus gallus (chicken)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 3.3 Å
AuthorsGruetter, C. / Richters, A. / Rauh, D.
CitationJournal: To be Published
Title: Overcoming Gatekeeper Mutations in cSrc and Abl by Hybrid Compound Design
Authors: Richters, A. / Getlik, M. / Gruetter, C. / Schneider, R. / Heuckmann, J.M. / Heynck, S. / Sos, M.L. / Thomas, R.K. / Rauh, D.
History
DepositionSep 27, 2011Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Oct 10, 2012Provider: repository / Type: Initial release
Revision 1.1Nov 1, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _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: Proto-oncogene tyrosine-protein kinase Src
B: Proto-oncogene tyrosine-protein kinase Src
hetero molecules


Theoretical massNumber of molelcules
Total (without water)66,7274
Polymers65,4852
Non-polymers1,2412
Water0
1
A: Proto-oncogene tyrosine-protein kinase Src
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,3632
Polymers32,7431
Non-polymers6211
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)33,3632
Polymers32,7431
Non-polymers6211
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)42.550, 64.280, 75.400
Angle α, β, γ (deg.)79.280, 87.380, 90.200
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: 32742.711 Da / Num. of mol.: 2 / Fragment: Kinase Domain, UNP residues 251-533 / Mutation: S345C
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Gallus gallus (chicken) / Gene: SRC, v-Src sarcoma viral oncogene / Plasmid: pSKB3 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: P00523, non-specific protein-tyrosine kinase
#2: Chemical ChemComp-AQB / N-(4-{[4-({[1-(3-aminophenyl)-3-tert-butyl-1H-pyrazol-5-yl]carbamoyl}amino)phenyl]amino}quinazolin-6-yl)-4-(dimethylamino)butanamide


Mass: 620.747 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C34H40N10O2

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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: 3.09 Å3/Da / Density % sol: 60.2 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 10% PEG 20000, 15% glycerol, 100mM MES, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: BRUKER AXS MICROSTAR / Wavelength: 1.5417 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: May 21, 2009 / Details: Osmic
RadiationMonochromator: Multilayer Optic / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5417 Å / Relative weight: 1
ReflectionResolution: 3.3→40 Å / Num. all: 11797 / Num. obs: 11298 / % possible obs: 95.8 % / Observed criterion σ(I): -3 / Redundancy: 2.21 % / Biso Wilson estimate: 18.547 Å2 / Rmerge(I) obs: 0.063 / Net I/σ(I): 15.24
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge F obsRmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique allNum. unique obsRrim(I) all% possible all
3.3-3.42.20.3330.1715.6420989989989540.23495.6
3.4-3.620.2130.1178.173882184317610.1695.6
3.62-4.420.1260.06713.78521403638690.09295.9
4.42-6.20.0870.04718.256676313630160.06496.2
6.2-80.0810.04120.1720229529190.05696.5
8-120.0340.02231.7712445825610.0396.4
12-160.0280.01736.063101461400.02395.9
16-400.0250.0238.45171104780.02775

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation3.3 Å28.58 Å
Translation3.3 Å28.58 Å

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
PHASER1.3.1phasing
REFMACrefinement
PDB_EXTRACT3.1data extraction
MAR345dtbdata collection
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3F3V

3f3v


Resolution: 3.3→28.58 Å / Cor.coef. Fo:Fc: 0.913 / Cor.coef. Fo:Fc free: 0.839 / WRfactor Rfree: 0.2198 / WRfactor Rwork: 0.1614 / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.8237 / SU B: 23.681 / SU ML: 0.397 / SU Rfree: 0.5484 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.548 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES: REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2563 678 6 %RANDOM
Rwork0.1889 10618 --
obs0.193 11296 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 60.95 Å2 / Biso mean: 24.4479 Å2 / Biso min: 2 Å2
Baniso -1Baniso -2Baniso -3
1--0.71 Å2-0.22 Å2-0.18 Å2
2--0.16 Å20.54 Å2
3---0.36 Å2
Refinement stepCycle: LAST / Resolution: 3.3→28.58 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4190 0 92 0 4282
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0224394
X-RAY DIFFRACTIONr_angle_refined_deg1.2241.9995958
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.5415516
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.32823.776196
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.0315756
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.6461530
X-RAY DIFFRACTIONr_chiral_restr0.080.2624
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0213356
X-RAY DIFFRACTIONr_mcbond_it0.4561.52596
X-RAY DIFFRACTIONr_mcangle_it0.86724198
X-RAY DIFFRACTIONr_scbond_it0.94131798
X-RAY DIFFRACTIONr_scangle_it1.7074.51760
LS refinement shellResolution: 3.3→3.385 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.407 49 -
Rwork0.276 771 -
all-820 -
obs--100 %

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