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- PDB-9w1a: Crystal structure of FGFR1 with a macrocyclic compound XS8148 -

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Basic information

Entry
Database: PDB / ID: 9w1a
TitleCrystal structure of FGFR1 with a macrocyclic compound XS8148
ComponentsFibroblast growth factor receptor 1
KeywordsTRANSFERASE / FGFR1
Function / homology
Function and homology information


Signaling by FGFR1 amplification mutants / diphosphate metabolic process / FGFR1c and Klotho ligand binding and activation / Signaling by plasma membrane FGFR1 fusions / cementum mineralization / chordate embryonic development / response to sodium phosphate / Epithelial-Mesenchymal Transition (EMT) during gastrulation / fibroblast growth factor receptor signaling pathway involved in orbitofrontal cortex development / ventricular zone neuroblast division ...Signaling by FGFR1 amplification mutants / diphosphate metabolic process / FGFR1c and Klotho ligand binding and activation / Signaling by plasma membrane FGFR1 fusions / cementum mineralization / chordate embryonic development / response to sodium phosphate / Epithelial-Mesenchymal Transition (EMT) during gastrulation / fibroblast growth factor receptor signaling pathway involved in orbitofrontal cortex development / ventricular zone neuroblast division / receptor-receptor interaction / positive regulation of phospholipase activity / FGFR1b ligand binding and activation / regulation of postsynaptic density assembly / Signaling by activated point mutants of FGFR1 / FGFR1c ligand binding and activation / Downstream signaling of activated FGFR1 / Phospholipase C-mediated cascade: FGFR1 / fibroblast growth factor receptor activity / skeletal system morphogenesis / positive regulation of vascular endothelial cell proliferation / positive regulation of endothelial cell chemotaxis / fibroblast growth factor receptor signaling pathway / Formation of paraxial mesoderm / PI-3K cascade:FGFR1 / positive regulation of MAP kinase activity / regulation of cell differentiation / phosphatidylinositol-mediated signaling / fibroblast growth factor binding / epithelial to mesenchymal transition / PI3K Cascade / skeletal system development / positive regulation of blood vessel endothelial cell migration / positive regulation of neuron differentiation / calcium ion homeostasis / SHC-mediated cascade:FGFR1 / FRS-mediated FGFR1 signaling / cellular response to fibroblast growth factor stimulus / positive regulation of cell cycle / peptidyl-tyrosine phosphorylation / Signaling by FGFR1 in disease / NCAM signaling for neurite out-growth / SH2 domain binding / Signal transduction by L1 / positive regulation of cell differentiation / neuron migration / Negative regulation of FGFR1 signaling / receptor protein-tyrosine kinase / Constitutive Signaling by Aberrant PI3K in Cancer / MAPK cascade / PIP3 activates AKT signaling / protein autophosphorylation / cell migration / heparin binding / PI5P, PP2A and IER3 Regulate PI3K/AKT Signaling / RAF/MAP kinase cascade / protein tyrosine kinase activity / cytoplasmic vesicle / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / positive regulation of MAPK cascade / protein phosphorylation / signaling receptor complex / postsynapse / positive regulation of cell population proliferation / negative regulation of transcription by RNA polymerase II / glutamatergic synapse / protein homodimerization activity / DNA-templated transcription / extracellular region / ATP binding / membrane / identical protein binding / nucleus / plasma membrane / cytosol
Similarity search - Function
Fibroblast growth factor receptor 1, catalytic domain / Fibroblast growth factor receptor family / Immunoglobulin / Immunoglobulin domain / Immunoglobulin I-set / Immunoglobulin I-set domain / : / Immunoglobulin subtype 2 / Immunoglobulin C-2 Type / Tyrosine-protein kinase, catalytic domain ...Fibroblast growth factor receptor 1, catalytic domain / Fibroblast growth factor receptor family / Immunoglobulin / Immunoglobulin domain / Immunoglobulin I-set / Immunoglobulin I-set domain / : / Immunoglobulin subtype 2 / Immunoglobulin C-2 Type / Tyrosine-protein kinase, catalytic domain / Tyrosine kinase, catalytic domain / Tyrosine protein kinases specific active-site signature. / Immunoglobulin subtype / Immunoglobulin / Tyrosine-protein kinase, active site / Protein tyrosine and serine/threonine kinase / Serine-threonine/tyrosine-protein kinase, catalytic domain / 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
: / Fibroblast growth factor receptor 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.96 Å
AuthorsChen, X.J. / Zhang, L. / Chen, Y.H.
Funding support China, 2items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)82172654 China
National Natural Science Foundation of China (NSFC)82202920 China
CitationJournal: To Be Published
Title: Crystal structure of FGFR1 with a macrocyclic compound XS8148
Authors: Chen, X.J. / Zhang, L. / Chen, Y.H.
History
DepositionJul 25, 2025Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Jul 29, 2026Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Fibroblast growth factor receptor 1
B: Fibroblast growth factor receptor 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)72,02210
Polymers70,5292
Non-polymers1,4938
Water5,026279
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)211.350, 49.780, 66.540
Angle α, β, γ (deg.)90.00, 107.48, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Fibroblast growth factor receptor 1 / FGFR-1 / Basic fibroblast growth factor receptor 1 / BFGFR / bFGF-R-1 / Fms-like tyrosine kinase 2 ...FGFR-1 / Basic fibroblast growth factor receptor 1 / BFGFR / bFGF-R-1 / Fms-like tyrosine kinase 2 / FLT-2 / N-sam / Proto-oncogene c-Fgr


Mass: 35264.520 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: FGFR1, BFGFR, CEK, FGFBR, FLG, FLT2, HBGFR / Production host: Escherichia coli (E. coli)
References: UniProt: P11362, receptor protein-tyrosine kinase
#2: Chemical ChemComp-A1EUM / XS8148


Mass: 458.473 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C23H22N8O3 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 279 / 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: 2.37 Å3/Da / Density % sol: 48.03 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop
Details: 20% (w/v) PEG 8000, 0.2 M Li2SO4, and 0.1 M MES, pH 6.5

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Data collection

DiffractionMean temperature: 80 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL10U2 / Wavelength: 0.97918 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: May 12, 2025
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 1.96→46.92 Å / Num. obs: 47054 / % possible obs: 98.34 % / Redundancy: 5.7 % / CC1/2: 0.997 / Rmerge(I) obs: 0.1117 / Net I/σ(I): 11.89
Reflection shellResolution: 1.96→2.03 Å / Rmerge(I) obs: 0.9822 / Mean I/σ(I) obs: 2.2 / Num. unique obs: 4422 / CC1/2: 0.653

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Processing

Software
NameVersionClassification
PHENIX(1.19.2_4158: ???)refinement
PDB_EXTRACTdata extraction
XDSdata reduction
XDSdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.96→46.92 Å / SU ML: 0.25 / Cross valid method: NONE / σ(F): 1.37 / Phase error: 25.36 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2448 2289 4.87 %
Rwork0.1951 --
obs0.1975 47009 98.35 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.96→46.92 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4603 0 98 279 4980
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0084795
X-RAY DIFFRACTIONf_angle_d0.966517
X-RAY DIFFRACTIONf_dihedral_angle_d7.937656
X-RAY DIFFRACTIONf_chiral_restr0.057709
X-RAY DIFFRACTIONf_plane_restr0.01834
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.96-20.3541310.29922554X-RAY DIFFRACTION91
2-2.050.33311500.27052725X-RAY DIFFRACTION97
2.05-2.10.27841270.24972808X-RAY DIFFRACTION98
2.1-2.160.27841710.23142739X-RAY DIFFRACTION99
2.16-2.220.24671360.21232783X-RAY DIFFRACTION99
2.22-2.290.26251330.21632834X-RAY DIFFRACTION99
2.29-2.370.28161650.20592817X-RAY DIFFRACTION99
2.37-2.470.26891480.21092790X-RAY DIFFRACTION100
2.47-2.580.2361530.21032793X-RAY DIFFRACTION100
2.58-2.720.2791290.20692830X-RAY DIFFRACTION100
2.72-2.890.26561420.20362853X-RAY DIFFRACTION100
2.89-3.110.2421370.20942822X-RAY DIFFRACTION99
3.11-3.420.23581430.18652835X-RAY DIFFRACTION99
3.42-3.920.20531570.17642830X-RAY DIFFRACTION99
3.92-4.940.21721340.15822842X-RAY DIFFRACTION98
4.94-46.920.24571330.18732865X-RAY DIFFRACTION96

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