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- PDB-8jf3: C-Src in complex with compound 9 -

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Basic information

Entry
Database: PDB / ID: 8jf3
TitleC-Src in complex with compound 9
ComponentsProto-oncogene tyrosine-protein kinase Src
KeywordsTRANSFERASE/Inhibitor / TRANSFERASE-Inhibitor complex
Function / homology
Function and homology information


regulation of caveolin-mediated endocytosis / cellular response to progesterone stimulus / positive regulation of dephosphorylation / regulation of toll-like receptor 3 signaling pathway / Regulation of commissural axon pathfinding by SLIT and ROBO / regulation of epithelial cell migration / negative regulation of telomere maintenance / Regulation of gap junction activity / ERBB2 signaling pathway / positive regulation of integrin activation ...regulation of caveolin-mediated endocytosis / cellular response to progesterone stimulus / positive regulation of dephosphorylation / regulation of toll-like receptor 3 signaling pathway / Regulation of commissural axon pathfinding by SLIT and ROBO / regulation of epithelial cell migration / negative regulation of telomere maintenance / Regulation of gap junction activity / ERBB2 signaling pathway / positive regulation of integrin activation / BMP receptor binding / negative regulation of focal adhesion assembly / Activated NTRK2 signals through FYN / intestinal epithelial cell development / Netrin mediated repulsion signals / negative regulation of neutrophil activation / positive regulation of small GTPase mediated signal transduction / focal adhesion assembly / connexin binding / Activated NTRK3 signals through PI3K / signal complex assembly / regulation of vascular permeability / Co-stimulation by CD28 / EPH-Ephrin signaling / podosome / positive regulation of lamellipodium morphogenesis / DCC mediated attractive signaling / regulation of bone resorption / Regulation of RUNX1 Expression and Activity / Ephrin signaling / Signal regulatory protein family interactions / negative regulation of mitochondrial depolarization / MET activates PTK2 signaling / leukocyte migration / Regulation of KIT signaling / cellular response to peptide hormone stimulus / regulation of early endosome to late endosome transport / Signaling by ALK / phospholipase activator activity / GP1b-IX-V activation signalling / Co-inhibition by CTLA4 / EPHA-mediated growth cone collapse / p130Cas linkage to MAPK signaling for integrins / interleukin-6-mediated signaling pathway / positive regulation of Notch signaling pathway / Receptor Mediated Mitophagy / stress fiber assembly / Signaling by EGFR / stimulatory C-type lectin receptor signaling pathway / negative regulation of intrinsic apoptotic signaling pathway / RUNX2 regulates osteoblast differentiation / Fc-gamma receptor signaling pathway involved in phagocytosis / PECAM1 interactions / GRB2:SOS provides linkage to MAPK signaling for Integrins / regulation of cell-cell adhesion / progesterone receptor signaling pathway / Recycling pathway of L1 / RHOU GTPase cycle / signaling receptor activator activity / positive regulation of epithelial cell migration / protein tyrosine kinase activator activity / RET signaling / FCGR activation / regulation of heart rate by cardiac conduction / negative regulation of anoikis / bone resorption / EPH-ephrin mediated repulsion of cells / Long-term potentiation / ephrin receptor signaling pathway / vascular endothelial growth factor receptor signaling pathway / GAB1 signalosome / negative regulation of hippo signaling / Nuclear signaling by ERBB4 / positive regulation of Rac protein signal transduction / negative regulation of protein-containing complex assembly / ephrin receptor binding / phospholipase binding / T cell costimulation / Signaling by ERBB2 / Integrin signaling / p38MAPK events / lactation / EPHB-mediated forward signaling / peptidyl-tyrosine phosphorylation / positive regulation of TORC1 signaling / osteoclast differentiation / transforming growth factor beta receptor signaling pathway / NCAM signaling for neurite out-growth / Downstream signal transduction / ionotropic glutamate receptor binding / FCGR3A-mediated IL10 synthesis / SH2 domain binding / response to interleukin-1 / positive regulation of glycolytic process / Downregulation of ERBB4 signaling / Signaling by phosphorylated juxtamembrane, extracellular and kinase domain KIT mutants / InlA-mediated entry of Listeria monocytogenes into host cells / integrin-mediated signaling pathway / negative regulation of extrinsic apoptotic signaling pathway / angiotensin-activated signaling pathway
Similarity search - Function
: / SH3 domain / SH2 domain / Src homology 2 (SH2) domain profile. / Src homology 2 domains / SH2 domain / Src homology 3 domains / SH2 domain superfamily / 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 / Src homology 3 domains / 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 / 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
: / Proto-oncogene tyrosine-protein kinase Src
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.84647631109 Å
AuthorsZhang, Z.M. / Huang, H.S.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Angew.Chem.Int.Ed.Engl. / Year: 2024
Title: Global Reactivity Profiling of the Catalytic Lysine in Human Kinome for Covalent Inhibitor Development.
Authors: Tang, G. / Wang, W. / Zhu, C. / Huang, H. / Chen, P. / Wang, X. / Xu, M. / Sun, J. / Zhang, C.J. / Xiao, Q. / Gao, L. / Zhang, Z.M. / Yao, S.Q.
History
DepositionMay 17, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 14, 2024Provider: repository / Type: Initial release
Revision 1.1Mar 27, 2024Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation_author.identifier_ORCID

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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)65,8684
Polymers64,7682
Non-polymers1,0992
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)41.716, 63.427, 73.649
Angle α, β, γ (deg.)101.214, 91.048, 90.161
Int Tables number1
Space group name H-MP1
Space group name HallP1
Symmetry operation#1: x,y,z

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Components

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


Mass: 32384.186 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SRC, SRC1 / Production host: Escherichia coli (E. coli)
References: UniProt: P12931, non-specific protein-tyrosine kinase
#2: Chemical ChemComp-C0N / 2-[4-[4-[bis(oxidanylidene)-$l^5-sulfanyl]oxyphenyl]carbonylpiperazin-1-yl]-6-[(5-cyclopropyl-1H-pyrazol-3-yl)amino]-N-prop-2-ynyl-pyrimidine-4-carboxamide


Mass: 549.582 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C25H25N8O5S
Has ligand of interestY

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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: 2.84 Å3/Da / Density % sol: 58.32 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 300 mM Sodium Acetate, 0.1 M MES pH 7.5, 4% PEG3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: CAMD / Beamline: GCPCC / Wavelength: 0.987 Å
DetectorType: DECTRIS PILATUS 300K / Detector: PIXEL / Date: Sep 9, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.987 Å / Relative weight: 1
ReflectionResolution: 2.84→72.23 Å / Num. obs: 16792 / % possible obs: 96.7 % / Redundancy: 3.1 % / Biso Wilson estimate: 34.3720629344 Å2 / CC1/2: 0.991 / Net I/σ(I): 5.5
Reflection shellResolution: 2.84→2.94 Å / Num. unique obs: 16792 / CC1/2: 0.894

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Processing

Software
NameVersionClassification
PHENIX1.9_1692+SVNrefinement
HKL-3000data reduction
HKL-3000data scaling
PHASERphasing
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.84647631109→62.2147194464 Å / SU ML: 0.506517564523 / Cross valid method: FREE R-VALUE / σ(F): 1.97311662566 / Phase error: 35.3254243612
RfactorNum. reflection% reflection
Rfree0.316930785964 1685 10.0477042338 %
Rwork0.274171879585 15085 -
obs0.278454516745 16770 96.5791292329 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 38.2139186642 Å2
Refinement stepCycle: LAST / Resolution: 2.84647631109→62.2147194464 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3775 0 78 0 3853
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.002707192095933949
X-RAY DIFFRACTIONf_angle_d0.6651841637585365
X-RAY DIFFRACTIONf_chiral_restr0.023116858326585
X-RAY DIFFRACTIONf_plane_restr0.00272214345272674
X-RAY DIFFRACTIONf_dihedral_angle_d14.99696651941441
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.8465-2.93020.3685344281941500.323628328151278X-RAY DIFFRACTION97.2089857046
2.9302-3.02480.3813210161831290.3158876952331267X-RAY DIFFRACTION97.6906927922
3.0248-3.13290.38701334921400.3145929112571263X-RAY DIFFRACTION97.3629424011
3.1329-3.25830.3506725142471420.3027414727291264X-RAY DIFFRACTION96.8319559229
3.2583-3.40660.3169446372041370.2728803077741257X-RAY DIFFRACTION96.9401947149
3.4066-3.58620.3370167570881410.2852152016071257X-RAY DIFFRACTION96.8814968815
3.5862-3.81090.338671375371480.276200742441278X-RAY DIFFRACTION96.2862930452
3.8109-4.10510.3020329359011410.2652101936111228X-RAY DIFFRACTION96.3406052076
4.1051-4.51810.3000479970571390.2455594891631267X-RAY DIFFRACTION96.169630643
4.5181-5.17160.2895401816851380.2467341570431242X-RAY DIFFRACTION96.1002785515
5.1716-6.51450.3068696644971420.2807359742681253X-RAY DIFFRACTION97.1448467967
6.5145-100.2579720212481380.2495165688211231X-RAY DIFFRACTION94.1540577717

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