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- PDB-9kfu: Human FGFR3 in complex with inhibitor F1 -

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Basic information

Entry
Database: PDB / ID: 9kfu
TitleHuman FGFR3 in complex with inhibitor F1
ComponentsFibroblast growth factor receptor 3
KeywordsTRANSFERASE / 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 / positive regulation of phospholipase activity / Signaling by activated point mutants of FGFR3 ...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 / positive regulation of phospholipase activity / Signaling by activated point mutants of FGFR3 / FGFR3c ligand binding and activation / Phospholipase C-mediated cascade; FGFR3 / endochondral ossification / fibroblast growth factor receptor activity / bone morphogenesis / positive regulation of tyrosine phosphorylation of STAT protein / PI-3K cascade:FGFR3 / bone mineralization / fibroblast growth factor binding / PI3K Cascade / fibroblast growth factor receptor signaling pathway / cell surface receptor signaling pathway via JAK-STAT / 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 / receptor protein-tyrosine kinase / Constitutive Signaling by Aberrant PI3K in Cancer / cell-cell signaling / PIP3 activates AKT signaling / MAPK cascade / PI5P, PP2A and IER3 Regulate PI3K/AKT Signaling / RAF/MAP kinase cascade / protein tyrosine kinase activity / positive regulation of ERK1 and ERK2 cascade / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / receptor complex / 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. / Immunoglobulin subtype / Immunoglobulin / Tyrosine-protein kinase, active site / 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: 1.4 Å
AuthorsZhang, J. / Song, K. / Li, M.Y.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: Nat Mach Intell / Year: 2025
Title: Electron-density-informed effective and reliable de novo molecular design and optimization with ED2Mol
Authors: Li, M. / Song, K. / He, J. / Zhao, M. / You, G. / Zhong, J. / Zhao, M. / Li, A. / Chen, Y. / Li, G. / Kong, Y. / Wei, J. / Wang, Z. / Zhou, J. / Yang, H. / Ma, S. / Zhang, H. / Melita, I.L. ...Authors: Li, M. / Song, K. / He, J. / Zhao, M. / You, G. / Zhong, J. / Zhao, M. / Li, A. / Chen, Y. / Li, G. / Kong, Y. / Wei, J. / Wang, Z. / Zhou, J. / Yang, H. / Ma, S. / Zhang, H. / Melita, I.L. / Lin, W. / Lu, Y. / Yu, Z. / Lu, X. / Zhao, Y. / Zhang, J.
History
DepositionNov 7, 2024Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 3, 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)35,4417
Polymers34,7341
Non-polymers7066
Water3,225179
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area220 Å2
ΔGint-18 kcal/mol
Surface area14270 Å2
MethodPISA
Unit cell
Length a, b, c (Å)71.610, 71.610, 153.760
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

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Components

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


Mass: 34734.051 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: FGFR3, JTK4 / Production host: Escherichia coli (E. coli)
References: UniProt: P22607, receptor protein-tyrosine kinase
#2: Chemical ChemComp-A1L5T / (7~{S})-2-azanyl-7-(4-fluorophenyl)-6,7-dihydro-4~{H}-[1,3]thiazolo[4,5-b]pyridin-5-one


Mass: 263.291 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C12H10FN3OS / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-CO / COBALT (II) ION


Mass: 58.933 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Co
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 179 / 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: 3.06 Å3/Da / Density % sol: 59.78 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: 25mM HEPES pH7.5, 1.8-2.0 M LiSO4, 10 Mm CoCl2

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Data collection

DiffractionMean temperature: 93 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.97791 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Dec 25, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97791 Å / Relative weight: 1
ReflectionResolution: 1.4→76.88 Å / Num. obs: 79055 / % possible obs: 100 % / Redundancy: 5.8 % / Rmerge(I) obs: 0.044 / Net I/σ(I): 7.8
Reflection shellResolution: 1.4→1.43 Å / Rmerge(I) obs: 0.196 / Num. unique obs: 3849

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Processing

Software
NameVersionClassification
REFMAC5.8.0430refinement
Cootmodel building
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.4→52.45 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.954 / SU B: 2.49 / SU ML: 0.082 / Cross valid method: THROUGHOUT / ESU R: 0.063 / ESU R Free: 0.065 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2509 3944 5 %RANDOM
Rwork0.22783 ---
obs0.22899 74982 99.97 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 27.25 Å2
Baniso -1Baniso -2Baniso -3
1-1.05 Å20 Å20 Å2
2--1.05 Å20 Å2
3----2.09 Å2
Refinement stepCycle: 1 / Resolution: 1.4→52.45 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2250 0 39 179 2468
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0122334
X-RAY DIFFRACTIONr_bond_other_d0.0020.0162253
X-RAY DIFFRACTIONr_angle_refined_deg1.9691.8453164
X-RAY DIFFRACTIONr_angle_other_deg0.7261.7735190
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0955286
X-RAY DIFFRACTIONr_dihedral_angle_2_deg7.639516
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.82310408
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.1380.2358
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.022699
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02511
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.7612.6481151
X-RAY DIFFRACTIONr_mcbond_other2.7542.6471150
X-RAY DIFFRACTIONr_mcangle_it3.9544.711431
X-RAY DIFFRACTIONr_mcangle_other3.9564.7131432
X-RAY DIFFRACTIONr_scbond_it3.9463.0651183
X-RAY DIFFRACTIONr_scbond_other3.8333.0181168
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.7535.3761709
X-RAY DIFFRACTIONr_long_range_B_refined8.75826.872587
X-RAY DIFFRACTIONr_long_range_B_other8.75226.332561
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.403→1.439 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.525 289 -
Rwork0.516 5447 -
obs--99.97 %

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