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- PDB-8jot: Crystal structure of CSF-1R kinase domain with sulfatinib -

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Basic information

Entry
Database: PDB / ID: 8jot
TitleCrystal structure of CSF-1R kinase domain with sulfatinib
ComponentsMacrophage colony-stimulating factor 1 receptor
KeywordsTRANSFERASE/INHIBITOR / sulfatinib / FGFR1 / DFG-out / TRANSFERASE / TRANSFERASE-INHIBITOR complex
Function / homology
Function and homology information


macrophage colony-stimulating factor receptor activity / forebrain neuron differentiation / CSF1-CSF1R complex / macrophage colony-stimulating factor signaling pathway / cell-cell junction maintenance / regulation of macrophage migration / cellular response to macrophage colony-stimulating factor stimulus / microglial cell proliferation / olfactory bulb development / mammary gland duct morphogenesis ...macrophage colony-stimulating factor receptor activity / forebrain neuron differentiation / CSF1-CSF1R complex / macrophage colony-stimulating factor signaling pathway / cell-cell junction maintenance / regulation of macrophage migration / cellular response to macrophage colony-stimulating factor stimulus / microglial cell proliferation / olfactory bulb development / mammary gland duct morphogenesis / positive regulation by host of viral process / ruffle organization / positive regulation of macrophage proliferation / regulation of bone resorption / positive regulation of cell motility / Other interleukin signaling / positive regulation of macrophage chemotaxis / cellular response to cytokine stimulus / regulation of MAPK cascade / cytokine binding / growth factor binding / monocyte differentiation / hemopoiesis / macrophage differentiation / positive regulation of protein tyrosine kinase activity / Transcriptional Regulation by VENTX / cell surface receptor protein tyrosine kinase signaling pathway / positive regulation of tyrosine phosphorylation of STAT protein / positive regulation of chemokine production / osteoclast differentiation / axon guidance / response to ischemia / regulation of actin cytoskeleton organization / receptor protein-tyrosine kinase / cytokine-mediated signaling pathway / peptidyl-tyrosine phosphorylation / Signaling by CSF1 (M-CSF) in myeloid cells / regulation of cell shape / protein tyrosine kinase activity / protein phosphatase binding / protein autophosphorylation / cell population proliferation / positive regulation of ERK1 and ERK2 cascade / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / receptor complex / positive regulation of cell migration / inflammatory response / positive regulation of protein phosphorylation / negative regulation of cell population proliferation / intracellular membrane-bounded organelle / innate immune response / positive regulation of cell population proliferation / negative regulation of apoptotic process / cell surface / signal transduction / protein homodimerization activity / nucleoplasm / ATP binding / plasma membrane
Similarity search - Function
Macrophage colony-stimulating factor 1 receptor / Tyrosine-protein kinase, receptor class III, conserved site / Receptor tyrosine kinase class III signature. / Immunoglobulin / Immunoglobulin domain / Immunoglobulin domain / : / Immunoglobulin subtype 2 / Immunoglobulin C-2 Type / Tyrosine-protein kinase, catalytic domain ...Macrophage colony-stimulating factor 1 receptor / Tyrosine-protein kinase, receptor class III, conserved site / Receptor tyrosine kinase class III signature. / Immunoglobulin / Immunoglobulin domain / Immunoglobulin domain / : / Immunoglobulin subtype 2 / Immunoglobulin C-2 Type / Tyrosine-protein kinase, catalytic domain / Tyrosine kinase, catalytic domain / Tyrosine protein kinases specific active-site signature. / Tyrosine-protein kinase, active site / Immunoglobulin subtype / Immunoglobulin / Serine-threonine/tyrosine-protein kinase, catalytic domain / Protein tyrosine and serine/threonine kinase / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Protein kinase, ATP binding site / Protein kinases ATP-binding region signature. / Immunoglobulin-like fold / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily
Similarity search - Domain/homology
: / Macrophage colony-stimulating factor 1 receptor
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.69 Å
AuthorsLin, Q.M. / Chen, X.J. / Chen, Y.H.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)82202920 China
CitationJournal: Commun Chem / Year: 2024
Title: Structural basis and selectivity of sulfatinib binding to FGFR and CSF-1R.
Authors: Lin, Q. / Dai, S. / Qu, L. / Lin, H. / Guo, M. / Wei, H. / Chen, Y. / Chen, X.
History
DepositionJun 8, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 27, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Macrophage colony-stimulating factor 1 receptor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,5133
Polymers39,9411
Non-polymers5732
Water5,621312
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area290 Å2
ΔGint-1 kcal/mol
Surface area14030 Å2
Unit cell
Length a, b, c (Å)64.310, 64.310, 184.685
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212
Components on special symmetry positions
IDModelComponents
11A-1381-

HOH

21A-1410-

HOH

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Components

#1: Protein Macrophage colony-stimulating factor 1 receptor / CSF-1 receptor / CSF-1-R / CSF-1R / M-CSF-R / Proto-oncogene c-Fms


Mass: 39940.656 Da / Num. of mol.: 1 / Mutation: C137T,C300S,C377T
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CSF1R, FMS / Production host: Spodoptera frugiperda (fall armyworm)
References: UniProt: P07333, receptor protein-tyrosine kinase
#2: Chemical ChemComp-UKI / N-(2-(dimethylamino)ethyl)-1-(3-((4-((2-methyl-1H-indol-5-yl)oxy)pyrimidin-2-yl)amino)phenyl)methanesulfonamide / Sulfatinib


Mass: 480.583 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C24H28N6O3S / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 312 / 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: 2.47 Å3/Da / Density % sol: 50.22 %
Crystal growTemperature: 277.15 K / Method: vapor diffusion, hanging drop / Details: 19% PEG8K, 0.2 M MgCl and 0.1 M Tris, pH 7.5

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Data collection

DiffractionMean temperature: 277.15 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 1.69 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jan 2, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.69 Å / Relative weight: 1
ReflectionResolution: 1.69→37.51 Å / Num. obs: 44396 / % possible obs: 99.7 % / Redundancy: 10.5 % / CC1/2: 0.993 / Net I/σ(I): 9.2
Reflection shellResolution: 1.69→1.75 Å / Rmerge(I) obs: 0.753 / Num. unique obs: 3092 / CC1/2: 0.463

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Processing

Software
NameVersionClassification
PHENIX(1.19.2_4158: ???)refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
PDB_EXTRACTdata extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4HW7

4hw7


Resolution: 1.69→36.58 Å / SU ML: 0.19 / Cross valid method: THROUGHOUT / σ(F): 1.43 / Phase error: 21.07 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2071 1998 4.51 %
Rwork0.179 --
obs0.1803 44287 99.63 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.69→36.58 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2370 0 40 312 2722
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0072470
X-RAY DIFFRACTIONf_angle_d0.8653352
X-RAY DIFFRACTIONf_dihedral_angle_d10.357346
X-RAY DIFFRACTIONf_chiral_restr0.057367
X-RAY DIFFRACTIONf_plane_restr0.007422
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.69-1.730.37411340.32632833X-RAY DIFFRACTION96
1.73-1.780.32751390.28652947X-RAY DIFFRACTION99
1.78-1.830.31841410.24132976X-RAY DIFFRACTION100
1.83-1.890.25051420.21922984X-RAY DIFFRACTION100
1.89-1.960.23831400.19412970X-RAY DIFFRACTION100
1.96-2.040.20691410.17232989X-RAY DIFFRACTION100
2.04-2.130.22251420.16383002X-RAY DIFFRACTION100
2.13-2.240.18981410.1762993X-RAY DIFFRACTION100
2.24-2.380.23131430.1763031X-RAY DIFFRACTION100
2.38-2.570.26521430.18173033X-RAY DIFFRACTION100
2.57-2.820.19451430.18253046X-RAY DIFFRACTION100
2.82-3.230.22731460.17613069X-RAY DIFFRACTION100
3.23-4.070.18021470.15263105X-RAY DIFFRACTION100
4.07-36.580.15531560.16863311X-RAY DIFFRACTION100

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