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- PDB-9vlj: Crystal structure of FGFR1 in complex with covalent inhibitor 10a -

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Basic information

Entry
Database: PDB / ID: 9vlj
TitleCrystal structure of FGFR1 in complex with covalent inhibitor 10a
ComponentsFibroblast growth factor receptor 1
KeywordsTRANSFERASE / FGFR1
Function / homology
Function and homology information


Signaling by FGFR1 amplification mutants / negative regulation of fibroblast growth factor production / positive regulation of mitotic cell cycle DNA replication / regulation of extrinsic apoptotic signaling pathway in absence of ligand / diphosphate metabolic process / Signaling by plasma membrane FGFR1 fusions / FGFR1c and Klotho ligand binding and activation / regulation of lateral mesodermal cell fate specification / positive regulation of MAPKKK cascade by fibroblast growth factor receptor signaling pathway / regulation of phosphate transport ...Signaling by FGFR1 amplification mutants / negative regulation of fibroblast growth factor production / positive regulation of mitotic cell cycle DNA replication / regulation of extrinsic apoptotic signaling pathway in absence of ligand / diphosphate metabolic process / Signaling by plasma membrane FGFR1 fusions / FGFR1c and Klotho ligand binding and activation / regulation of lateral mesodermal cell fate specification / positive regulation of MAPKKK cascade by fibroblast growth factor receptor signaling pathway / regulation of phosphate transport / vitamin D3 metabolic process / cementum mineralization / regulation of branching involved in salivary gland morphogenesis by mesenchymal-epithelial signaling / 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 / mesenchymal cell proliferation / positive regulation of phospholipase activity / receptor-receptor interaction / chordate embryonic development / positive regulation of parathyroid hormone secretion / auditory receptor cell development / paraxial mesoderm development / regulation of postsynaptic density assembly / FGFR1b ligand binding and activation / organ induction / Signaling by activated point mutants of FGFR1 / FGFR1c ligand binding and activation / Downstream signaling of activated FGFR1 / fibroblast growth factor receptor activity / Phospholipase C-mediated cascade: FGFR1 / branching involved in salivary gland morphogenesis / lung-associated mesenchyme development / cell projection assembly / outer ear morphogenesis / embryonic limb morphogenesis / positive regulation of vascular endothelial cell proliferation / positive regulation of endothelial cell chemotaxis / ureteric bud development / positive regulation of mesenchymal cell proliferation / skeletal system morphogenesis / inner ear morphogenesis / middle ear morphogenesis / Formation of paraxial mesoderm / positive regulation of stem cell proliferation / PI-3K cascade:FGFR1 / midbrain development / positive regulation of MAP kinase activity / phosphatidylinositol-mediated signaling / regulation of cell differentiation / fibroblast growth factor binding / fibroblast growth factor receptor signaling pathway / PI3K Cascade / epithelial to mesenchymal transition / positive regulation of blood vessel endothelial cell migration / chondrocyte differentiation / cardiac muscle cell proliferation / positive regulation of cardiac muscle cell proliferation / calcium ion homeostasis / SHC-mediated cascade:FGFR1 / peptidyl-tyrosine phosphorylation / FRS-mediated FGFR1 signaling / cell maturation / cellular response to fibroblast growth factor stimulus / positive regulation of neuron differentiation / Signaling by FGFR1 in disease / NCAM signaling for neurite out-growth / SH2 domain binding / stem cell proliferation / stem cell differentiation / Signal transduction by L1 / skeletal system development / positive regulation of cell differentiation / Negative regulation of FGFR1 signaling / sensory perception of sound / receptor protein-tyrosine kinase / positive regulation of neuron projection development / neuron migration / Constitutive Signaling by Aberrant PI3K in Cancer / neuron projection development / protein autophosphorylation / PIP3 activates AKT signaling / MAPK cascade / cell migration / heparin binding / PI5P, PP2A and IER3 Regulate PI3K/AKT Signaling / RAF/MAP kinase cascade / protein tyrosine kinase activity / angiogenesis / cytoplasmic vesicle / gene expression / in utero embryonic development / protein phosphorylation / positive regulation of MAPK cascade / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / signaling receptor complex / postsynapse / positive regulation of cell population proliferation / glutamatergic synapse
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: 1.81 Å
AuthorsChen, X.J. / Liu, X.R. / Zhang, L. / Chen, Y.H.
Funding support China, 2items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)82202920 China
National Natural Science Foundation of China (NSFC)82172654 China
CitationJournal: J.Med.Chem. / Year: 2026
Title: Structure-Based Design of 4-(1-Methyl-1 H -indol-3-yl)pyrimidin-2-amine Derivatives as the First Covalent FGFR3 Selective Inhibitors.
Authors: Zhu, W. / Chen, X. / Li, X. / Lin, J. / Lin, X. / Liu, X. / Deng, W. / Song, X. / Tu, Z. / Patterson, A.V. / Smaill, J.B. / Chen, Y. / Lu, X.
History
DepositionJun 25, 2025Deposition site: PDBJ / Processing site: PDBC
Revision 1.0May 6, 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)72,56114
Polymers70,5292
Non-polymers2,03212
Water7,620423
1
A: Fibroblast growth factor receptor 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,3778
Polymers35,2651
Non-polymers1,1127
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Fibroblast growth factor receptor 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,1846
Polymers35,2651
Non-polymers9205
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)211.440, 49.710, 66.840
Angle α, β, γ (deg.)90.00, 107.75, 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-A1ESP / ~{N}-[3-[2-[[3-[2-(dimethylamino)ethylsulfamoylmethyl]phenyl]amino]pyrimidin-4-yl]-1-methyl-indol-6-yl]propanamide


Mass: 535.661 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C27H33N7O3S / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 423 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
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: 2.37 Å3/Da / Density % sol: 48.14 %
Crystal growTemperature: 277.15 K / Method: vapor diffusion, hanging drop
Details: 18% (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: BL02U1 / Wavelength: 0.97918 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 13, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 1.81→36.99 Å / Num. obs: 60085 / % possible obs: 99.04 % / Redundancy: 6.3 % / CC1/2: 0.996 / Rmerge(I) obs: 0.1604 / Net I/σ(I): 10.05
Reflection shellResolution: 1.81→1.875 Å / Redundancy: 4.8 % / Rmerge(I) obs: 1.64 / Mean I/σ(I) obs: 1.75 / Num. unique obs: 28223 / CC1/2: 0.453 / % possible all: 98.13

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Processing

Software
NameVersionClassification
PHENIX(1.19.2_4158: ???)refinement
PDB_EXTRACTdata extraction
xia2data reduction
xia2data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.81→31.6 Å / SU ML: 0.22 / Cross valid method: NONE / σ(F): 1.35 / Phase error: 21.92 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2146 3006 5 %
Rwork0.1762 --
obs0.1781 60083 99.07 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.81→31.6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4666 0 126 423 5215
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0094891
X-RAY DIFFRACTIONf_angle_d1.0516643
X-RAY DIFFRACTIONf_dihedral_angle_d9.279668
X-RAY DIFFRACTIONf_chiral_restr0.067714
X-RAY DIFFRACTIONf_plane_restr0.011845
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.81-1.840.31331310.28182674X-RAY DIFFRACTION99
1.84-1.870.32361400.26882638X-RAY DIFFRACTION98
1.87-1.910.35011070.25962728X-RAY DIFFRACTION98
1.91-1.940.34541410.25562670X-RAY DIFFRACTION99
1.94-1.980.21191220.22682694X-RAY DIFFRACTION98
1.98-2.020.25091260.2042696X-RAY DIFFRACTION99
2.02-2.070.2211340.18992713X-RAY DIFFRACTION99
2.07-2.120.25011460.18242677X-RAY DIFFRACTION99
2.12-2.180.2041470.17192691X-RAY DIFFRACTION99
2.18-2.250.23511660.17782691X-RAY DIFFRACTION99
2.25-2.320.23251790.17582686X-RAY DIFFRACTION99
2.32-2.40.20721590.17332694X-RAY DIFFRACTION99
2.4-2.50.18791460.16742738X-RAY DIFFRACTION99
2.5-2.610.20511450.16872721X-RAY DIFFRACTION99
2.61-2.750.23911600.16882705X-RAY DIFFRACTION100
2.75-2.920.24481610.18152744X-RAY DIFFRACTION100
2.92-3.140.1911320.17672747X-RAY DIFFRACTION100
3.14-3.460.20141440.16112739X-RAY DIFFRACTION100
3.46-3.960.19971300.15712795X-RAY DIFFRACTION100
3.96-4.990.18481370.14682804X-RAY DIFFRACTION100
4.99-31.60.18781530.18192832X-RAY DIFFRACTION99

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