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- PDB-9d1x: Crystal structure of FGFR3 bound to indazole inhibitor -

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Basic information

Entry
Database: PDB / ID: 9d1x
TitleCrystal structure of FGFR3 bound to indazole inhibitor
ComponentsFibroblast growth factor receptor 3
KeywordsCELL CYCLE / fibroblast growth factor receptor 3 / inhibitor
Function / homology
Function and homology information


t(4;14) translocations of FGFR3 / negative regulation of developmental growth / fibroblast growth factor receptor apoptotic signaling pathway / Signaling by FGFR3 fusions in cancer / bone maturation / chondrocyte proliferation / endochondral bone growth / FGFR3b ligand binding and activation / Signaling by activated point mutants of FGFR3 / FGFR3c ligand binding and activation ...t(4;14) translocations of FGFR3 / negative regulation of developmental growth / fibroblast growth factor receptor apoptotic signaling pathway / Signaling by FGFR3 fusions in cancer / bone maturation / chondrocyte proliferation / endochondral bone growth / FGFR3b ligand binding and activation / Signaling by activated point mutants of FGFR3 / FGFR3c ligand binding and activation / Phospholipase C-mediated cascade; FGFR3 / endochondral ossification / positive regulation of phospholipase activity / bone morphogenesis / positive regulation of tyrosine phosphorylation of STAT protein / PI-3K cascade:FGFR3 / bone mineralization / fibroblast growth factor binding / PI3K Cascade / cell surface receptor signaling pathway via JAK-STAT / fibroblast growth factor receptor signaling pathway / chondrocyte differentiation / SHC-mediated cascade:FGFR3 / transport vesicle / FRS-mediated FGFR3 signaling / Signaling by FGFR3 in disease / skeletal system development / Negative regulation of FGFR3 signaling / placental growth factor receptor activity / insulin receptor activity / vascular endothelial growth factor receptor activity / hepatocyte growth factor receptor activity / macrophage colony-stimulating factor receptor activity / platelet-derived growth factor alpha-receptor activity / platelet-derived growth factor beta-receptor activity / stem cell factor receptor activity / boss receptor activity / protein tyrosine kinase collagen receptor activity / brain-derived neurotrophic factor receptor activity / transmembrane-ephrin receptor activity / GPI-linked ephrin receptor activity / epidermal growth factor receptor activity / fibroblast growth factor receptor activity / insulin-like growth factor receptor activity / receptor protein-tyrosine kinase / Constitutive Signaling by Aberrant PI3K in Cancer / MAPK cascade / cell-cell signaling / PIP3 activates AKT signaling / RAF/MAP kinase cascade / PI5P, PP2A and IER3 Regulate PI3K/AKT Signaling / protein tyrosine kinase activity / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / receptor complex / positive regulation of ERK1 and ERK2 cascade / positive regulation of MAPK cascade / positive regulation of cell population proliferation / cell surface / endoplasmic reticulum / Golgi apparatus / extracellular region / ATP binding / identical protein binding / plasma membrane
Similarity search - Function
Fibroblast growth factor receptor 3 transmembrane domain / Fibroblast growth factor receptor family / 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 ...Fibroblast growth factor receptor 3 transmembrane domain / Fibroblast growth factor receptor family / 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. / 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
: / Fibroblast growth factor receptor 3
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsPostel, S. / Johnson, Z.L.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Chemrxiv / Year: 2024
Title: OPLS5: Addition of Polarizability and Improved Treatment of Metals
Authors: Damm, W. / Dajnowicz, S. / Ghoreishi, D. / Yu, Y. / Ganeshan, K. / Madin, O. / Rudshteyn, B. / Hu, R. / Wu, M. / Shang, Y. / Albanese, S. / Zou, Y. / Ye, M. / Johnson, Z. / Trzoss, M. / ...Authors: Damm, W. / Dajnowicz, S. / Ghoreishi, D. / Yu, Y. / Ganeshan, K. / Madin, O. / Rudshteyn, B. / Hu, R. / Wu, M. / Shang, Y. / Albanese, S. / Zou, Y. / Ye, M. / Johnson, Z. / Trzoss, M. / Rafi, S. / Kapilashrami, K. / Saleh, N. / Ghanakota, P. / Zhang, Y. / Sampson, J. / Chen, W. / Wang, L. / Dahlgren, M. / Russell, E. / Leffler, A. / Abel, R. / Friesner, R. / Harder, E.
History
DepositionAug 8, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 25, 2025Provider: 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 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,1774
Polymers33,7421
Non-polymers4353
Water3,765209
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)55.870, 55.870, 365.784
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number179
Space group name H-MP6522

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Components

#1: Protein Fibroblast growth factor receptor 3 / FGFR-3


Mass: 33742.016 Da / Num. of mol.: 1 / Fragment: kinase domain / Mutation: P572S, P573G
Source method: isolated from a genetically manipulated source
Details: residues 572-585 replaced with a Ser-Gly linker, C-terminal His6 tag
Source: (gene. exp.) Homo sapiens (human) / Gene: FGFR3, JTK4 / Cell line (production host): Sf21 / Production host: Spodoptera frugiperda (fall armyworm)
References: UniProt: P22607, receptor protein-tyrosine kinase
#2: Chemical ChemComp-A1A6M / (3P)-N-(2,6-dimethylphenyl)-6-methoxy-3-(1-methyl-1H-pyrazol-4-yl)-1H-indazole-5-carboxamide


Mass: 375.424 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H21N5O2 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 209 / 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: 2.44 Å3/Da / Density % sol: 49.63 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.1
Details: 0.2 M magnesium chloride, 0.3 M sodium chloride, 23% (w/v) PEG 3350, 0.1 M Tris-HCl pH 8.1

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1 Å
DetectorType: DECTRIS EIGER2 S 16M / Detector: PIXEL / Date: Nov 27, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.6→33.25 Å / Num. obs: 46623 / % possible obs: 100 % / Redundancy: 31 % / CC1/2: 0.999 / Rmerge(I) obs: 0.123 / Rpim(I) all: 0.022 / Rrim(I) all: 0.125 / Χ2: 0.84 / Net I/σ(I): 15.6 / Num. measured all: 1444088
Reflection shellResolution: 1.6→1.63 Å / Redundancy: 28.1 % / Rmerge(I) obs: 1.084 / Mean I/σ(I) obs: 2.2 / Num. unique obs: 2209 / CC1/2: 0.925 / Rpim(I) all: 0.199 / Rrim(I) all: 1.103 / Χ2: 0.32 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.20.1refinement
Aimlessdata scaling
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.6→33.23 Å / Cross valid method: FREE R-VALUE
RfactorNum. reflection% reflection
Rfree0.1903 --
Rwork0.1801 --
obs-46441 100 %
Refinement stepCycle: LAST / Resolution: 1.6→33.23 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2234 0 30 209 2473

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