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- PDB-6ate: SRC kinase bound to covalent inhibitor -

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Basic information

Entry
Database: PDB / ID: 6ate
TitleSRC kinase bound to covalent inhibitor
ComponentsProto-oncogene tyrosine-protein kinase Src
KeywordsTRANSFERASE/TRANSFERASE INHIBITOR / KINASE / PHOSPHORYLATION / TRANSFERASE-TRANSFERASE INHIBITOR COMPLEX / TRANSFERASE
Function / homology
Function and homology information


regulation of caveolin-mediated endocytosis / regulation of toll-like receptor 3 signaling pathway / cellular response to progesterone stimulus / positive regulation of platelet-derived growth factor receptor-beta signaling pathway / 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 / cellular response to progesterone stimulus / positive regulation of platelet-derived growth factor receptor-beta signaling pathway / 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 / osteoclast development / Activated NTRK3 signals through PI3K / 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 / positive regulation of lamellipodium morphogenesis / regulation of bone resorption / Ephrin signaling / Signal regulatory protein family interactions / negative regulation of mitochondrial depolarization / odontogenesis / podosome / MET activates PTK2 signaling / cellular response to peptide hormone stimulus / Regulation of KIT signaling / regulation of early endosome to late endosome transport / Signaling by ALK / leukocyte migration / phospholipase activator activity / oogenesis / Co-inhibition by CTLA4 / EPHA-mediated growth cone collapse / GP1b-IX-V activation signalling / Receptor Mediated Mitophagy / p130Cas linkage to MAPK signaling for integrins / interleukin-6-mediated signaling pathway / stress fiber assembly / Signaling by EGFR / positive regulation of Notch signaling pathway / RUNX2 regulates osteoblast differentiation / negative regulation of intrinsic apoptotic signaling pathway / stimulatory C-type lectin receptor signaling pathway / Fc-gamma receptor signaling pathway involved in phagocytosis / forebrain development / Recycling pathway of L1 / PECAM1 interactions / regulation of cell-cell adhesion / uterus development / GRB2:SOS provides linkage to MAPK signaling for Integrins / regulation of heart rate by cardiac conduction / RHOU GTPase cycle / protein tyrosine kinase activator activity / RET signaling / signaling receptor activator activity / negative regulation of anoikis / Long-term potentiation / FCGR activation / positive regulation of epithelial cell migration / progesterone receptor signaling pathway / EPH-ephrin mediated repulsion of cells / positive regulation of protein serine/threonine kinase activity / GAB1 signalosome / negative regulation of hippo signaling / ephrin receptor signaling pathway / vascular endothelial growth factor receptor signaling pathway / bone resorption / negative regulation of protein-containing complex assembly / Downregulation of ERBB4 signaling / Nuclear signaling by ERBB4 / InlA-mediated entry of Listeria monocytogenes into host cells / phospholipase binding / ephrin receptor binding / T cell costimulation / cellular response to platelet-derived growth factor stimulus / p38MAPK events / Signaling by ERBB2 / EPHB-mediated forward signaling / Integrin signaling / ionotropic glutamate receptor binding / positive regulation of TORC1 signaling / NCAM signaling for neurite out-growth
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-6H3 / Proto-oncogene tyrosine-protein kinase Src
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.402 Å
AuthorsGurbani, D. / Westover, K.D.
CitationJournal: Cell Chem Biol / Year: 2019
Title: Leveraging Compound Promiscuity to Identify Targetable Cysteines within the Kinome.
Authors: Rao, S. / Gurbani, D. / Du, G. / Everley, R.A. / Browne, C.M. / Chaikuad, A. / Tan, L. / Schroder, M. / Gondi, S. / Ficarro, S.B. / Sim, T. / Kim, N.D. / Berberich, M.J. / Knapp, S. / Marto, ...Authors: Rao, S. / Gurbani, D. / Du, G. / Everley, R.A. / Browne, C.M. / Chaikuad, A. / Tan, L. / Schroder, M. / Gondi, S. / Ficarro, S.B. / Sim, T. / Kim, N.D. / Berberich, M.J. / Knapp, S. / Marto, J.A. / Westover, K.D. / Sorger, P.K. / Gray, N.S.
History
DepositionAug 28, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 27, 2019Provider: repository / Type: Initial release
Revision 2.0Dec 18, 2019Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / citation / citation_author / entity / pdbx_poly_seq_scheme / pdbx_refine_tls_group / pdbx_struct_sheet_hbond / pdbx_unobs_or_zero_occ_residues / pdbx_validate_close_contact / pdbx_validate_torsion / struct_conf / struct_conn / struct_mon_prot_cis / struct_ref_seq / struct_ref_seq_dif / struct_sheet_range / struct_site_gen
Item: _atom_site.auth_seq_id / _atom_site_anisotrop.pdbx_auth_seq_id ..._atom_site.auth_seq_id / _atom_site_anisotrop.pdbx_auth_seq_id / _citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _entity.pdbx_fragment / _pdbx_poly_seq_scheme.pdb_seq_num / _pdbx_refine_tls_group.beg_auth_asym_id / _pdbx_refine_tls_group.beg_auth_seq_id / _pdbx_refine_tls_group.end_auth_asym_id / _pdbx_refine_tls_group.end_auth_seq_id / _pdbx_refine_tls_group.selection_details / _pdbx_struct_sheet_hbond.range_1_auth_seq_id / _pdbx_struct_sheet_hbond.range_2_auth_seq_id / _pdbx_unobs_or_zero_occ_residues.auth_seq_id / _pdbx_validate_close_contact.auth_seq_id_1 / _pdbx_validate_close_contact.auth_seq_id_2 / _pdbx_validate_torsion.auth_seq_id / _struct_conf.beg_auth_seq_id / _struct_conf.end_auth_seq_id / _struct_conn.ptnr1_auth_seq_id / _struct_mon_prot_cis.auth_seq_id / _struct_mon_prot_cis.pdbx_auth_seq_id_2 / _struct_ref_seq.pdbx_auth_seq_align_beg / _struct_ref_seq.pdbx_auth_seq_align_end / _struct_ref_seq_dif.pdbx_auth_seq_num / _struct_sheet_range.beg_auth_seq_id / _struct_sheet_range.end_auth_seq_id / _struct_site_gen.auth_seq_id
Revision 2.1Oct 4, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 2.2Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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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)33,1772
Polymers32,7111
Non-polymers4661
Water1,15364
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)41.510, 62.758, 105.892
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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


Mass: 32710.582 Da / Num. of mol.: 1
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-6H3 / N-{2-[(5-chloro-2-{[4-(4-methylpiperazin-1-yl)phenyl]amino}pyrimidin-4-yl)amino]phenyl}propanamide


Mass: 465.978 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C24H28ClN7O
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 64 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.11 Å3/Da / Density % sol: 41.66 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 0.1 M MES, pH 6.5, 16%-20% PEG 3350, 350 mM - 420mM NaOAc

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.979 Å
DetectorType: DECTRIS PILATUS3 X 6M / Detector: PIXEL / Date: Jun 15, 2017
RadiationMonochromator: YES / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.4→50 Å / Num. obs: 10871 / % possible obs: 96 % / Redundancy: 9.9 % / Rmerge(I) obs: 0.093 / Net I/σ(I): 1.4
Reflection shellResolution: 2.4→2.44 Å / Rmerge(I) obs: 0.448 / Num. unique obs: 381 / CC1/2: 0.767

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Processing

Software
NameVersionClassification
PHENIX(1.12rc1_2807: ???)refinement
HKL-3000data reduction
SCALEPACKdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4YBK

4ybk


Resolution: 2.402→40.468 Å / SU ML: 0.3 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 23.85 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2282 544 5 %
Rwork0.193 --
obs0.1947 10871 96.03 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.402→40.468 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2058 0 33 64 2155
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0022143
X-RAY DIFFRACTIONf_angle_d0.5062898
X-RAY DIFFRACTIONf_dihedral_angle_d12.7621284
X-RAY DIFFRACTIONf_chiral_restr0.041308
X-RAY DIFFRACTIONf_plane_restr0.003367
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4023-2.6440.2981170.24992237X-RAY DIFFRACTION85
2.644-3.02640.281390.23452635X-RAY DIFFRACTION100
3.0264-3.81250.22111410.19022662X-RAY DIFFRACTION100
3.8125-40.47380.20691470.1732793X-RAY DIFFRACTION99
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.98320.06922.43.95220.13295.34410.1370.7702-0.4833-0.8460.08950.16970.88460.5632-0.16030.9476-0.02930.03470.7397-0.11010.5446-1.5209-32.4035-1.6051
23.37040.08010.33154.09230.56483.4663-0.0630.341-0.2151-0.44980.0668-0.33240.07150.1912-0.02150.29-0.0280.05570.2324-0.03040.30531.0708-26.912615.5895
34.56561.13920.31724.7474-0.50062.1573-0.0308-0.31750.03510.02030.07880.2694-0.0148-0.4588-0.050.25270.03470.03520.3378-0.01430.2788-9.0426-24.913226.9443
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND RESID 260:337 )A260 - 337
2X-RAY DIFFRACTION2( CHAIN A AND RESID 338:405 )A338 - 405
3X-RAY DIFFRACTION3( CHAIN A AND RESID 406:536 )A406 - 536

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