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- PDB-7d57: C-Src in complex with FIIN-2 -

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Basic information

Entry
Database: PDB / ID: 7d57
TitleC-Src in complex with FIIN-2
ComponentsProto-oncogene tyrosine-protein kinase Src
KeywordsTRANSFERASE / TRANSFERASE INHIBITOR
Function / homology
Function and homology information


Signaling by ERBB2 / Nuclear signaling by ERBB4 / PIP3 activates AKT signaling / Signaling by SCF-KIT / Regulation of KIT signaling / Signaling by EGFR / GAB1 signalosome / Regulation of gap junction activity / FCGR activation / PECAM1 interactions ...Signaling by ERBB2 / Nuclear signaling by ERBB4 / PIP3 activates AKT signaling / Signaling by SCF-KIT / Regulation of KIT signaling / Signaling by EGFR / GAB1 signalosome / Regulation of gap junction activity / FCGR activation / PECAM1 interactions / CD28 co-stimulation / CTLA4 inhibitory signaling / 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 / RAF activation / PI5P, PP2A and IER3 Regulate PI3K/AKT Signaling / RET signaling / Receptor Mediated Mitophagy / ADP signalling through P2Y purinoceptor 1 / Downregulation of ERBB4 signaling / EPH-ephrin mediated repulsion of cells / Cyclin D associated events in G1 / Regulation of RUNX3 expression and activity / Activated NTRK3 signals through PI3K / Downstream signal transduction / 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 / osteoclast development / progesterone receptor signaling pathway / negative regulation of intrinsic apoptotic signaling pathway / bone resorption / extrinsic component of cytoplasmic side of plasma membrane / negative regulation of extrinsic apoptotic signaling pathway / non-specific protein-tyrosine kinase / non-membrane spanning protein tyrosine kinase activity / epidermal growth factor receptor signaling pathway / cell junction / protein phosphatase binding / protein tyrosine kinase activity / mitochondrial inner membrane / cell differentiation / cytoskeleton / endosome membrane / cell adhesion / regulation of cell cycle / cell cycle / phosphorylation / innate immune response / focal adhesion / signaling receptor binding / heme binding / perinuclear region of cytoplasm / protein-containing complex / ATP binding / membrane / nucleus / plasma membrane / cytosol
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 / 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
Chem-37O / Proto-oncogene tyrosine-protein kinase Src
Similarity search - Component
Biological speciesGallus gallus (chicken)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.104 Å
AuthorsChen, Y.H. / Qu, L.Z.
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 25, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 13, 2021Provider: repository / Type: Initial release
Revision 1.1Mar 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 1.2Nov 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

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)66,9196
Polymers65,4532
Non-polymers1,4664
Water5,459303
1
A: Proto-oncogene tyrosine-protein kinase Src
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,5564
Polymers32,7271
Non-polymers8293
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area190 Å2
ΔGint-14 kcal/mol
Surface area12720 Å2
MethodPISA
2
B: Proto-oncogene tyrosine-protein kinase Src
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,3632
Polymers32,7271
Non-polymers6371
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area12510 Å2
MethodPISA
Unit cell
Length a, b, c (Å)41.798, 62.964, 74.138
Angle α, β, γ (deg.)78.980, 89.780, 89.690
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-37O / N-(4-{[3-(3,5-dimethoxyphenyl)-7-{[4-(4-methylpiperazin-1-yl)phenyl]amino}-2-oxo-3,4-dihydropyrimido[4,5-d]pyrimidin-1(2H)-yl]methyl}phenyl)propanamide


Mass: 636.743 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C35H40N8O4 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 303 / 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: 2.92 Å3/Da / Density % sol: 57.9 %
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 315r / 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: 2.1→27.405 Å / Num. obs: 35316 / % possible obs: 96.74 % / Redundancy: 3.2 % / CC1/2: 0.98 / Net I/σ(I): 11.5
Reflection shellResolution: 2.1→2.2 Å / Num. unique obs: 4487 / CC1/2: 0.68

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Processing

Software
NameVersionClassification
PHENIX1.11.1_2575refinement
PDB_EXTRACT3.25data extraction
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4U5J

4u5j


Resolution: 2.104→27.405 Å / SU ML: 0.24 / Cross valid method: THROUGHOUT / σ(F): 2.03 / Phase error: 25.34 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2221 1988 5.63 %
Rwork0.1853 33305 -
obs0.1874 35293 82.1 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 143.51 Å2 / Biso mean: 42.4445 Å2 / Biso min: 12.76 Å2
Refinement stepCycle: final / Resolution: 2.104→27.405 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4070 0 104 303 4477
Biso mean--58.82 42.7 -
Num. residues----514
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0094289
X-RAY DIFFRACTIONf_angle_d0.8675825
X-RAY DIFFRACTIONf_chiral_restr0.046619
X-RAY DIFFRACTIONf_plane_restr0.005736
X-RAY DIFFRACTIONf_dihedral_angle_d12.2442609
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.1043-2.15690.2915580.228289731
2.1569-2.21520.2581710.2319126344
2.2152-2.28030.2695840.2373144450
2.2803-2.35390.28451310.2272209372
2.3539-2.4380.28531480.2235253587
2.438-2.53550.26361580.2111264092
2.5355-2.65090.23881680.2043279796
2.6509-2.79050.25071670.1988278396
2.7905-2.96510.25791700.1953284198
2.9651-3.19370.23061710.1962281698
3.1937-3.51460.20061680.1788279997
3.5146-4.02170.21311630.167278096
4.0217-5.06180.18671670.1549276395
5.0618-27.4050.18561640.1744285498
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)
10.47110.00090.13012.2113-0.71844.00610.11770.31240.0236-0.8235-0.1432-0.1611-0.1450.08180.05410.49180.06250.02980.30740.00790.2433-11.57714.7384-47.5991
21.93590.4637-0.3442.8357-0.50461.8890.0112-0.1263-0.1173-0.1193-0.1685-0.29020.04380.36680.07290.13950.03470.00780.2050.02880.1871-3.7964-3.5147-26.1018
30.37150.4053-1.04352.8853-0.9742.82110.0618-0.29990.40610.7122-0.11360.0419-1.54140.38310.09371.1795-0.0737-0.10240.4066-0.00730.3706-8.846938.27846.2768
41.15721.07460.2761.30081.01255.36-0.1808-0.30730.1320.77840.04360.175-0.0587-0.63070.11880.67760.01530.01890.45090.05840.2263-13.554727.42060.7806
51.0006-0.56020.2142.50880.33792.0707-0.0258-0.12980.21640.5730.0085-0.1756-0.2462-0.0284-0.02240.3405-0.0341-0.03530.1754-0.01670.2457-9.441831.1686-11.3412
64.1991-0.2597-0.33953.1573-0.60151.74930.028-0.15240.00230.5614-0.00480.3734-0.1582-0.5016-0.04140.2-0.0170.01980.3167-0.04440.2741-23.704730.6407-17.2703
70.47850.55290.10763.2527-0.01261.91480.17230.40.2915-0.2181-0.14580.542-0.2191-0.56530.02940.20990.062-0.03130.3749-0.00570.2865-21.397336.2815-29.5818
81.1731-1.48390.53363.70740.09551.5586-0.00790.2953-0.2263-0.2725-0.13320.10290.099-0.21640.12330.1875-0.06910.00260.2232-0.06160.1975-13.703521.2612-26.8539
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 258 through 359 )A258 - 359
2X-RAY DIFFRACTION2chain 'A' and (resid 360 through 533 )A360 - 533
3X-RAY DIFFRACTION3chain 'B' and (resid 257 through 308 )B257 - 308
4X-RAY DIFFRACTION4chain 'B' and (resid 309 through 329 )B309 - 329
5X-RAY DIFFRACTION5chain 'B' and (resid 330 through 402 )B330 - 402
6X-RAY DIFFRACTION6chain 'B' and (resid 403 through 456 )B403 - 456
7X-RAY DIFFRACTION7chain 'B' and (resid 457 through 488 )B457 - 488
8X-RAY DIFFRACTION8chain 'B' and (resid 489 through 533 )B489 - 533

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