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- PDB-7d5o: C-Src in complex with TAS-120 -

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Basic information

Entry
Database: PDB / ID: 7d5o
TitleC-Src in complex with TAS-120
ComponentsProto-oncogene tyrosine-protein kinase Src
KeywordsTRANSFERASE / TRANSFERASE INHIBITOR
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-TZ0 / Proto-oncogene tyrosine-protein kinase Src
Similarity search - Component
Biological speciesGallus gallus (chicken)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.69 Å
AuthorsQu, L.Z. / Chen, Y.H.
Funding support China, 3items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)81570537 China
National Natural Science Foundation of China (NSFC)81974074 China
National Natural Science Foundation of China (NSFC)31900880 China
CitationJournal: Commun Chem / Year: 2022
Title: Structural insights into the potency and selectivity of covalent pan-FGFR inhibitors
Authors: Qu, L. / Chen, X. / Wei, H. / Guo, M. / Dai, S. / Jiang, L. / Li, J. / Yue, S. / Chen, Z. / Chen, Y.
History
DepositionSep 27, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 22, 2021Provider: repository / Type: Initial release
Revision 2.0Feb 9, 2022Group: Advisory / Atomic model ...Advisory / Atomic model / Author supporting evidence / Data collection / Derived calculations / Non-polymer description / Refinement description / Source and taxonomy / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / atom_type / chem_comp / entity / entity_src_gen / pdbx_contact_author / pdbx_entity_instance_feature / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_refine_tls / pdbx_refine_tls_group / pdbx_struct_sheet_hbond / pdbx_validate_close_contact / pdbx_validate_planes / pdbx_validate_rmsd_angle / pdbx_validate_symm_contact / pdbx_validate_torsion / refine / refine_hist / refine_ls_restr / refine_ls_shell / software / struct_conf / struct_mon_prot_cis / struct_sheet / struct_sheet_order / struct_sheet_range
Item: _chem_comp.formula / _chem_comp.formula_weight ..._chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.pdbx_synonyms / _chem_comp.type / _entity.pdbx_description / _entity.pdbx_number_of_molecules / _entity_src_gen.gene_src_common_name / _pdbx_contact_author.email / _pdbx_contact_author.id / _pdbx_contact_author.identifier_ORCID / _pdbx_contact_author.name_first / _pdbx_contact_author.name_last / _pdbx_entity_instance_feature.auth_comp_id / _pdbx_entity_instance_feature.comp_id / _pdbx_entity_nonpoly.comp_id / _pdbx_entity_nonpoly.name / _refine.B_iso_max / _refine.B_iso_mean / _refine.B_iso_min / _refine.ls_R_factor_R_free / _refine.ls_R_factor_R_work / _refine.ls_R_factor_obs / _refine.ls_d_res_high / _refine.ls_d_res_low / _refine.overall_SU_ML / _refine.pdbx_overall_phase_error / _refine_hist.d_res_high / _refine_hist.d_res_low / _refine_hist.number_atoms_solvent / _refine_hist.number_atoms_total / _refine_hist.pdbx_B_iso_mean_ligand / _refine_hist.pdbx_B_iso_mean_solvent / _refine_ls_shell.R_factor_R_free / _refine_ls_shell.R_factor_R_work / _refine_ls_shell.d_res_high / _refine_ls_shell.d_res_low / _refine_ls_shell.number_reflns_all / _refine_ls_shell.pdbx_total_number_of_bins_used / _software.version / _struct_mon_prot_cis.pdbx_omega_angle / _struct_sheet.number_strands
Description: Ligand identity / Provider: author / Type: Coordinate replacement
Revision 2.1Mar 9, 2022Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.pdbx_database_id_DOI / _citation.title / _citation.year
Revision 2.2Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)66,2904
Polymers65,4532
Non-polymers8372
Water1,04558
1
B: Proto-oncogene tyrosine-protein kinase Src
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,1452
Polymers32,7271
Non-polymers4181
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Proto-oncogene tyrosine-protein kinase Src
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,1452
Polymers32,7271
Non-polymers4181
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)41.969, 63.184, 73.137
Angle α, β, γ (deg.)100.640, 90.610, 89.820
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: 32726.645 Da / Num. of mol.: 2
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-TZ0 / 1-[(3S)-3-{4-amino-3-[(3,5-dimethoxyphenyl)ethynyl]-1H-pyrazolo[3,4-d]pyrimidin-1-yl}pyrrolidin-1-yl]prop-2-en-1-one


Mass: 418.448 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C22H22N6O3 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 58 / Source method: isolated from a natural source / Formula: H2O
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: 2.91 Å3/Da / Density % sol: 57.76 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6.4
Details: 2% glycerol, 8% PEG 4000, 50mM sodium acetate, 10mM MgCl2

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.97915 Å
DetectorType: ADSC QUANTUM 1 / Detector: CCD / Date: May 31, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97915 Å / Relative weight: 1
ReflectionResolution: 2.685→28.88 Å / Num. obs: 19833 / % possible obs: 96.05 % / Redundancy: 3.3 % / CC1/2: 0.985 / Net I/σ(I): 9.33
Reflection shellResolution: 2.685→2.781 Å / Num. unique obs: 1589 / CC1/2: 0.767

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
PDB_EXTRACT3.25data extraction
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4U5J

4u5j


Resolution: 2.69→28.88 Å / SU ML: 0.36 / Cross valid method: THROUGHOUT / σ(F): 1.98 / Phase error: 26.06 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2369 1979 9.98 %
Rwork0.1784 17849 -
obs0.1844 19828 96.13 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 120.56 Å2 / Biso mean: 52.164 Å2 / Biso min: 17.93 Å2
Refinement stepCycle: final / Resolution: 2.69→28.88 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3974 0 62 58 4094
Biso mean--63.73 47.87 -
Num. residues----501
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.69-2.750.35411090.2721921103069
2.75-2.830.33091410.25531288142995
2.83-2.910.32911380.21811283142197
2.91-30.30071420.21851312145498
3-3.110.31381420.21181276141898
3.11-3.240.28031460.23031324147099
3.24-3.380.26651400.19211277141799
3.38-3.560.22781450.17421309145499
3.56-3.780.23951490.16841340148999
3.78-4.070.22841470.15991287143498
4.07-4.480.16941440.14011299144397
4.48-5.130.18881500.14571309145999
5.13-6.450.23221440.1831312145699
6.45-28.880.21011420.16441312145499

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