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- PDB-2bdj: Src kinase in complex with inhibitor AP23464 -

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Basic information

Entry
Database: PDB / ID: 2bdj
TitleSrc kinase in complex with inhibitor AP23464
ComponentsProto-oncogene tyrosine-protein kinase Src
KeywordsTRANSFERASE / Src kinase Inhibitor
Function / homology
Function and homology information


regulation of caveolin-mediated endocytosis / regulation of toll-like receptor 3 signaling pathway / positive regulation of platelet-derived growth factor receptor-beta signaling pathway / cellular response to progesterone stimulus / positive regulation of dephosphorylation / regulation of cell projection assembly / negative regulation of telomere maintenance / Regulation of commissural axon pathfinding by SLIT and ROBO / regulation of epithelial cell migration / ERBB2 signaling pathway ...regulation of caveolin-mediated endocytosis / regulation of toll-like receptor 3 signaling pathway / positive regulation of platelet-derived growth factor receptor-beta signaling pathway / cellular response to progesterone stimulus / positive regulation of dephosphorylation / regulation of cell projection assembly / negative regulation of telomere maintenance / Regulation of commissural axon pathfinding by SLIT and ROBO / regulation of epithelial cell migration / ERBB2 signaling pathway / Regulation of gap junction activity / BMP receptor binding / negative regulation of focal adhesion assembly / positive regulation of integrin activation / Activated NTRK2 signals through FYN / positive regulation of protein processing / Netrin mediated repulsion signals / regulation of intracellular estrogen receptor signaling pathway / intestinal epithelial cell development / negative regulation of neutrophil activation / regulation of vascular permeability / focal adhesion assembly / connexin binding / Activated NTRK3 signals through PI3K / osteoclast development / cellular response to fluid shear stress / signal complex assembly / positive regulation of small GTPase mediated signal transduction / branching involved in mammary gland duct morphogenesis / Co-stimulation by CD28 / Regulation of RUNX1 Expression and Activity / DCC mediated attractive signaling / EPH-Ephrin signaling / positive regulation of podosome assembly / regulation of bone resorption / positive regulation of lamellipodium morphogenesis / Ephrin signaling / Signal regulatory protein family interactions / podosome / odontogenesis / negative regulation of mitochondrial depolarization / MET activates PTK2 signaling / cellular response to peptide hormone stimulus / Regulation of KIT signaling / regulation of early endosome to late endosome transport / leukocyte migration / Signaling by ALK / phospholipase activator activity / oogenesis / GP1b-IX-V activation signalling / Co-inhibition by CTLA4 / EPHA-mediated growth cone collapse / Receptor Mediated Mitophagy / p130Cas linkage to MAPK signaling for integrins / interleukin-6-mediated signaling pathway / stress fiber assembly / positive regulation of Notch signaling pathway / Signaling by EGFR / RUNX2 regulates osteoblast differentiation / stimulatory C-type lectin receptor signaling pathway / negative regulation of intrinsic apoptotic signaling pathway / Fc-gamma receptor signaling pathway involved in phagocytosis / regulation of cell-cell adhesion / Recycling pathway of L1 / PECAM1 interactions / uterus development / regulation of heart rate by cardiac conduction / GRB2:SOS provides linkage to MAPK signaling for Integrins / RHOU GTPase cycle / protein tyrosine kinase activator activity / RET signaling / negative regulation of anoikis / Long-term potentiation / signaling receptor activator activity / FCGR activation / positive regulation of epithelial cell migration / EPH-ephrin mediated repulsion of cells / positive regulation of protein serine/threonine kinase activity / GAB1 signalosome / negative regulation of hippo signaling / vascular endothelial growth factor receptor signaling pathway / ephrin receptor signaling pathway / bone resorption / negative regulation of protein-containing complex assembly / forebrain development / Downregulation of ERBB4 signaling / progesterone receptor signaling pathway / Nuclear signaling by ERBB4 / InlA-mediated entry of Listeria monocytogenes into host cells / phospholipase binding / T cell costimulation / cellular response to platelet-derived growth factor stimulus / p38MAPK events / ephrin receptor binding / Signaling by ERBB2 / EPHB-mediated forward signaling / Integrin signaling / positive regulation of TORC1 signaling / NCAM signaling for neurite out-growth / ionotropic glutamate receptor binding
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 / 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-HET / Proto-oncogene tyrosine-protein kinase Src
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsDalgarno, D. / Stehle, T. / Schelling, P. / Narula, S. / Sawyer, T.
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

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Assembly

Deposited unit
A: Proto-oncogene tyrosine-protein kinase Src
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,4452
Polymers31,9701
Non-polymers4761
Water2,900161
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)42.1, 54.6, 69.0
Angle α, β, γ (deg.)90, 99.97, 90
Int Tables number4
Space group name H-MP1211

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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.: 1 / 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-HET / 3-[2-(2-CYCLOPENTYL-6-{[4-(DIMETHYLPHOSPHORYL)PHENYL]AMINO}-9H-PURIN-9-YL)ETHYL]PHENOL


Mass: 475.522 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C26H30N5O2P
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 161 / 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: 2.44 Å3/Da / Density % sol: 49.63 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.3
Details: 20% PEG3350, 200mM NH4NO3, pH 6.3, 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 2, 2002
RadiationMonochromator: Mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.5→50 Å / Num. obs: 9800 / % possible obs: 90.6 % / 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: 2.5→20 Å / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.277 980 10% of data
Rwork0.158 --
obs-9800 -
Refinement stepCycle: LAST / Resolution: 2.5→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2048 0 34 161 2243

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