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- PDB-2bdf: Src kinase in complex with inhibitor AP23451 -

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Basic information

Entry
Database: PDB / ID: 2bdf
TitleSrc kinase in complex with inhibitor AP23451
ComponentsProto-oncogene tyrosine-protein kinase Src
KeywordsTRANSFERASE / Src Kinase Inhibitor
Function / homology
Function and homology information


regulation of toll-like receptor 3 signaling pathway / positive regulation of non-membrane spanning protein tyrosine kinase activity / primary ovarian follicle growth / regulation of caveolin-mediated endocytosis / positive regulation of ovarian follicle development / cellular response to prolactin / positive regulation of platelet-derived growth factor receptor-beta signaling pathway / positive regulation of male germ cell proliferation / dendritic filopodium / regulation of cell projection assembly ...regulation of toll-like receptor 3 signaling pathway / positive regulation of non-membrane spanning protein tyrosine kinase activity / primary ovarian follicle growth / regulation of caveolin-mediated endocytosis / positive regulation of ovarian follicle development / cellular response to prolactin / positive regulation of platelet-derived growth factor receptor-beta signaling pathway / positive regulation of male germ cell proliferation / dendritic filopodium / regulation of cell projection assembly / regulation of cell-cell adhesion / positive regulation of dephosphorylation / response to mineralocorticoid / Regulation of commissural axon pathfinding by SLIT and ROBO / ERBB2 signaling pathway / regulation of epithelial cell migration / positive regulation of protein transport / Regulation of gap junction activity / regulation of vascular permeability / entry of bacterium into host cell / BMP receptor binding / positive regulation of lamellipodium morphogenesis / cellular response to progesterone stimulus / positive regulation of integrin activation / Activated NTRK2 signals through FYN / negative regulation of focal adhesion assembly / skeletal muscle cell proliferation / positive regulation of protein processing / negative regulation of telomerase activity / Netrin mediated repulsion signals / regulation of intracellular estrogen receptor signaling pathway / intestinal epithelial cell development / CD28 co-stimulation / positive regulation of glucose metabolic process / transcytosis / Activated NTRK3 signals through PI3K / connexin binding / cellular response to fluid shear stress / focal adhesion assembly / signal complex assembly / response to acidic pH / podosome / positive regulation of small GTPase mediated signal transduction / positive regulation of Ras protein signal transduction / positive regulation of podosome assembly / Regulation of RUNX1 Expression and Activity / regulation of bone resorption / branching involved in mammary gland duct morphogenesis / DCC mediated attractive signaling / negative regulation of mitochondrial depolarization / adherens junction organization / osteoclast development / myoblast proliferation / EPH-Ephrin signaling / Ephrin signaling / odontogenesis / cellular response to peptide hormone stimulus / Signal regulatory protein family interactions / cellular response to fatty acid / MET activates PTK2 signaling / regulation of early endosome to late endosome transport / oogenesis / Receptor Mediated Mitophagy / GP1b-IX-V activation signalling / Regulation of KIT signaling / Signaling by ALK / postsynaptic specialization, intracellular component / CTLA4 inhibitory signaling / Signaling by EGFR / phospholipase activator activity / leukocyte migration / DNA biosynthetic process / EPHA-mediated growth cone collapse / Fc-gamma receptor signaling pathway involved in phagocytosis / interleukin-6-mediated signaling pathway / p130Cas linkage to MAPK signaling for integrins / negative regulation of hippo signaling / positive regulation of epithelial cell migration / positive regulation of Notch signaling pathway / stress fiber assembly / cellular response to platelet-derived growth factor stimulus / positive regulation of smooth muscle cell migration / regulation of heart rate by cardiac conduction / Recycling pathway of L1 / RUNX2 regulates osteoblast differentiation / progesterone receptor signaling pathway / dendritic growth cone / stimulatory C-type lectin receptor signaling pathway / negative regulation of telomere maintenance via telomerase / uterus development / PECAM1 interactions / phospholipase binding / neurotrophin TRK receptor signaling pathway / Long-term potentiation / GRB2:SOS provides linkage to MAPK signaling for Integrins / RHOU GTPase cycle / platelet-derived growth factor receptor signaling pathway / FCGR activation / EPH-ephrin mediated repulsion of cells / negative regulation of anoikis
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 ...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 / 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-24A / Proto-oncogene tyrosine-protein kinase Src
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsDalgarno, D. / Stehle, T. / Schelling, P. / Sawyer, T. / Narula, S.
CitationJournal: Chem.Biol.Drug Des. / Year: 2006
Title: Structural basis of Src tyrosine kinase inhibition with a new class of potent and selective trisubstituted purine-based compounds.
Authors: Dalgarno, D. / Stehle, T. / Narula, S. / Schelling, P. / van Schravendijk, M.R. / Adams, S. / Andrade, L. / Keats, J. / Ram, M. / Jin, L. / Grossman, T. / MacNeil, I. / Metcalf III, C. / ...Authors: Dalgarno, D. / Stehle, T. / Narula, S. / Schelling, P. / van Schravendijk, M.R. / Adams, S. / Andrade, L. / Keats, J. / Ram, M. / Jin, L. / Grossman, T. / MacNeil, I. / Metcalf III, C. / Shakespeare, W. / Wang, Y. / Keenan, T. / Sundaramoorthi, R. / Bohacek, R. / Weigele, M. / Sawyer, T.
History
DepositionOct 20, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 24, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 23, 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_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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)64,9284
Polymers63,9402
Non-polymers9892
Water9,044502
1
A: Proto-oncogene tyrosine-protein kinase Src
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,4642
Polymers31,9701
Non-polymers4941
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Proto-oncogene tyrosine-protein kinase Src
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,4642
Polymers31,9701
Non-polymers4941
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)41.930, 59.740, 63.590
Angle α, β, γ (deg.)93.03, 91.43, 97.79
Int Tables number1
Space group name H-MP1

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Components

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


Mass: 31969.771 Da / Num. of mol.: 2 / Fragment: kinase domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SRC, SRC1 / Cell line (production host): SF-9 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P12931, EC: 2.7.1.112
#2: Chemical ChemComp-24A / {[(4-{[2-(4-AMINOCYCLOHEXYL)-9-ETHYL-9H-PURIN-6-YL]AMINO}PHENYL)(HYDROXY)PHOSPHORYL]METHYL}PHOSPHONIC ACID


Mass: 494.421 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C20H28N6O5P2
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 502 / 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: 2.46 Å3/Da / Density % sol: 50.04 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 15% PEG400, 50mM NaCl, 100mM HEPES pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 298 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU300 / Wavelength: 1.5418
DetectorType: RIGAKU RAXIS II / Detector: IMAGE PLATE / Date: Jan 1, 2002
RadiationMonochromator: Mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.1→50 Å / Num. obs: 59170 / % possible obs: 82.9 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
X-PLOR3.1refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry 1FMK

1fmk


Resolution: 2.1→20 Å / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.271 5917 10% of data
Rwork0.206 --
obs-59170 -
Refinement stepCycle: LAST / Resolution: 2.1→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4233 0 66 502 4801

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