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- PDB-10dj: Fyn Kinase Domain-Saracatinib Complex Structure -

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Basic information

Entry
Database: PDB / ID: 10dj
TitleFyn Kinase Domain-Saracatinib Complex Structure
ComponentsTyrosine-protein kinase Fyn
KeywordsSIGNALING PROTEIN / Tyrosine-protein kinase Fyn
Function / homology
Function and homology information


negative regulation of hydrogen peroxide biosynthetic process / response to singlet oxygen / Reelin signalling pathway / perinuclear endoplasmic reticulum / NTRK2 activates RAC1 / regulation of glutamate receptor signaling pathway / Activated NTRK2 signals through FYN / heart process / SEMA3A-Plexin repulsion signaling by inhibiting Integrin adhesion / regulation of calcium ion import across plasma membrane ...negative regulation of hydrogen peroxide biosynthetic process / response to singlet oxygen / Reelin signalling pathway / perinuclear endoplasmic reticulum / NTRK2 activates RAC1 / regulation of glutamate receptor signaling pathway / Activated NTRK2 signals through FYN / heart process / SEMA3A-Plexin repulsion signaling by inhibiting Integrin adhesion / regulation of calcium ion import across plasma membrane / Platelet Adhesion to exposed collagen / reelin-mediated signaling pathway / CRMPs in Sema3A signaling / FLT3 signaling through SRC family kinases / G protein-coupled glutamate receptor signaling pathway / activated T cell proliferation / type 5 metabotropic glutamate receptor binding / positive regulation of protein localization to membrane / CD4 receptor binding / feeding behavior / Nef and signal transduction / cellular response to L-glutamate / Co-stimulation by CD28 / EPH-Ephrin signaling / Nephrin family interactions / natural killer cell activation / DCC mediated attractive signaling / negative regulation of dendritic spine maintenance / Ephrin signaling / CD28 dependent Vav1 pathway / dendritic spine maintenance / cellular response to peptide hormone stimulus / growth factor receptor binding / Regulation of KIT signaling / leukocyte migration / phospholipase activator activity / tau-protein kinase activity / negative regulation of T cell activation / EPHA-mediated growth cone collapse / Co-inhibition by CTLA4 / dendrite morphogenesis / peptide hormone receptor binding / Dectin-2 family / stimulatory C-type lectin receptor signaling pathway / Fc-gamma receptor signaling pathway involved in phagocytosis / forebrain development / CD8 receptor binding / PECAM1 interactions / response to amyloid-beta / FCGR activation / negative regulation of T cell receptor signaling pathway / Sema3A PAK dependent Axon repulsion / cellular response to glycine / CD28 dependent PI3K/Akt signaling / EPH-ephrin mediated repulsion of cells / Role of LAT2/NTAL/LAB on calcium mobilization / negative regulation of extrinsic apoptotic signaling pathway in absence of ligand / vascular endothelial growth factor receptor signaling pathway / positive regulation of protein targeting to membrane / ephrin receptor signaling pathway / detection of mechanical stimulus involved in sensory perception of pain / cellular response to transforming growth factor beta stimulus / glial cell projection / alpha-tubulin binding / negative regulation of oxidative stress-induced intrinsic apoptotic signaling pathway / postsynaptic density, intracellular component / phosphatidylinositol 3-kinase binding / ephrin receptor binding / GPVI-mediated activation cascade / phospholipase binding / T cell receptor binding / T cell costimulation / cellular response to platelet-derived growth factor stimulus / Signaling by ERBB2 / EPHB-mediated forward signaling / peptidyl-tyrosine phosphorylation / NCAM signaling for neurite out-growth / CD209 (DC-SIGN) signaling / negative regulation of protein ubiquitination / FCGR3A-mediated IL10 synthesis / cell surface receptor protein tyrosine kinase signaling pathway / Antigen activates B Cell Receptor (BCR) leading to generation of second messengers / axon guidance / Signaling by phosphorylated juxtamembrane, extracellular and kinase domain KIT mutants / negative regulation of angiogenesis / Cell surface interactions at the vascular wall / learning / protein catabolic process / FCGR3A-mediated phagocytosis / non-specific protein-tyrosine kinase / response to cocaine / actin filament / Regulation of signaling by CBL / negative regulation of inflammatory response to antigenic stimulus / non-membrane spanning protein tyrosine kinase activity / Signaling by SCF-KIT / positive regulation of neuron projection development / Degradation of CDH1 / negative regulation of protein catabolic process / G protein-coupled receptor binding
Similarity search - Function
: / Fyn/Yrk, 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 ...: / Fyn/Yrk, 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 / Serine-threonine/tyrosine-protein kinase, catalytic domain / Protein tyrosine and serine/threonine kinase / 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-H8H / Tyrosine-protein kinase Fyn
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.22 Å
AuthorsTa, H.M. / MacKenzie, K. / Ferreon, J.C. / Ferreon, A.C. / Kim, C.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS) United States
CitationJournal: Int J Mol Sci / Year: 2026
Title: Fyn-Saracatinib Complex Structure Reveals an Active State-like Conformation
Authors: Ta, H.M. / Sankaran, B. / Roush, E.D. / Ferreon, J.C. / Ferreon, A.C.M. / Kim, C.
History
DepositionJan 13, 2026Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 18, 2026Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Tyrosine-protein kinase Fyn
B: Tyrosine-protein kinase Fyn
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,8304
Polymers64,7462
Non-polymers1,0842
Water8,251458
1
A: Tyrosine-protein kinase Fyn
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,9152
Polymers32,3731
Non-polymers5421
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Tyrosine-protein kinase Fyn
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,9152
Polymers32,3731
Non-polymers5421
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)79.687, 89.601, 92.010
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Components on special symmetry positions
IDModelComponents
11B-904-

HOH

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Components

#1: Protein Tyrosine-protein kinase Fyn / Proto-oncogene Syn / Proto-oncogene c-Fyn / Src-like kinase / SLK / p59-Fyn


Mass: 32373.193 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: FYN / Production host: Spodoptera frugiperda (fall armyworm)
References: UniProt: P06241, non-specific protein-tyrosine kinase
#2: Chemical ChemComp-H8H / N-(5-CHLORO-1,3-BENZODIOXOL-4-YL)-7-[2-(4-METHYLPIPERAZIN-1-YL)ETHOXY]-5-(TETRAHYDRO-2H-PYRAN-4-YLOXY)QUINAZOLIN-4-AMINE / SARACATINIB


Mass: 542.026 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C27H32ClN5O5 / Feature type: SUBJECT OF INVESTIGATION / Comment: inhibitor*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 458 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN

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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: 2.62 Å3/Da / Density % sol: 53.13 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop
Details: 4.0 M ammonium acetate, 0.1 M sodium acetate trihydrate, pH 4.6

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSLS-II / Beamline: 17-ID-2 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Jan 15, 2025
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.22→33.85 Å / Num. obs: 33168 / % possible obs: 99.69 % / Redundancy: 8.6 % / CC1/2: 0.991 / Net I/σ(I): 4
Reflection shellResolution: 2.22→2.28 Å / Num. unique obs: 2691 / CC1/2: 0.462

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Processing

Software
NameVersionClassification
PHENIX("2.0_5885": ???)refinement
XSCALEdata scaling
HKL-2000data reduction
PHENIXphasing
PDB_EXTRACTdata extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.22→33.85 Å / SU ML: 0.35 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 33.58 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2681 1651 4.98 %
Rwork0.2447 --
obs0.2459 33163 99.69 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.22→33.85 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4332 0 76 458 4866
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0044522
X-RAY DIFFRACTIONf_angle_d0.7616131
X-RAY DIFFRACTIONf_dihedral_angle_d15.5621681
X-RAY DIFFRACTIONf_chiral_restr0.047656
X-RAY DIFFRACTIONf_plane_restr0.005773
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.22-2.280.40711340.37262557X-RAY DIFFRACTION99
2.28-2.360.38321310.34932620X-RAY DIFFRACTION100
2.36-2.440.33521360.33662563X-RAY DIFFRACTION100
2.44-2.540.34941370.31352603X-RAY DIFFRACTION100
2.54-2.660.34181350.31032601X-RAY DIFFRACTION100
2.66-2.80.34121340.28692597X-RAY DIFFRACTION100
2.8-2.970.31071400.26912621X-RAY DIFFRACTION100
2.97-3.20.24141370.24022614X-RAY DIFFRACTION100
3.2-3.520.24461370.21382620X-RAY DIFFRACTION100
3.52-4.030.21891370.1782660X-RAY DIFFRACTION100
4.03-5.070.16351430.17022670X-RAY DIFFRACTION100
5.08-33.850.2891500.25052786X-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)
11.54440.915-1.73994.8258-2.12936.13410.316-0.20570.24560.0825-0.4906-0.2023-0.8491-0.00030.00110.65-0.0538-0.00130.29620.02070.4425-11.068924.2891-21.1497
21.19790.55-2.03852.5912-1.76294.7244-0.0041-0.03520.1280.0145-0.0122-0.0052-0.03460.20740.06880.41860.0023-0.09540.285-0.0160.2928-17.546813.1786-11.8819
32.6416-0.7383-0.34813.20243.74574.49840.30950.78670.0675-1.3988-0.49340.27560.0603-0.3140.1540.8165-0.0161-0.10980.5435-0.02560.3617-24.2603-0.6996-20.9906
42.683-0.2284-0.85524.2110.51795.0674-0.30840.1555-0.23520.0210.2053-0.07850.6110.06550.04460.54180.0306-0.04940.28110.03190.264-23.8458-3.9522-1.7284
54.0314-1.3607-0.80535.34030.81156.47320.2937-0.0221-0.19840.3241-0.30580.29020.76570.10310.02280.43580.0451-0.03950.2280.04110.2866-9.0846-44.5313-27.9572
61.0995-1.32471.72551.7647-1.2913.18580.02110.0082-0.043-0.2978-0.06670.03150.2410.0705-0.01020.3419-0.0386-0.01240.23640.01320.267-19.0162-35.5303-35.0222
70.318-0.3751-1.47671.91730.169.1093-0.5826-1.15950.58840.87240.6618-0.1206-0.00030.94240.01340.77420.1821-0.15120.5879-0.11110.4008-21.9919-20.0183-27.279
81.93340.34550.03384.5940.44294.99360.0189-0.07490.3015-0.0657-0.0574-0.0258-0.82840.12210.03250.2590.043-0.06290.23880.0040.2356-23.7955-18.903-44.0782
90.17710.5597-0.89327.2998-0.47296.19740.70420.42840.26971.07180.6841-0.0906-0.4268-1.0264-0.76010.90470.00190.15920.56360.17710.3735-17-52.7617-42.194
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 263 through 276 )
2X-RAY DIFFRACTION2chain 'A' and (resid 277 through 406 )
3X-RAY DIFFRACTION3chain 'A' and (resid 407 through 426 )
4X-RAY DIFFRACTION4chain 'A' and (resid 427 through 531 )
5X-RAY DIFFRACTION5chain 'B' and (resid 263 through 301 )
6X-RAY DIFFRACTION6chain 'B' and (resid 302 through 411 )
7X-RAY DIFFRACTION7chain 'B' and (resid 412 through 434 )
8X-RAY DIFFRACTION8chain 'B' and (resid 435 through 527 )
9X-RAY DIFFRACTION9chain 'B' and (resid 533 through 544 )

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