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- PDB-9vmb: The X-RAY co-crystal structure of human FGFR3 and Compound 10t -

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Basic information

Entry
Database: PDB / ID: 9vmb
TitleThe X-RAY co-crystal structure of human FGFR3 and Compound 10t
ComponentsFibroblast growth factor receptor 3
KeywordsTRANSFERASE / FGFR3
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 / positive regulation of phospholipase activity / 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 / fibroblast growth factor receptor signaling pathway / PI3K Cascade / chondrocyte differentiation / cell surface receptor signaling pathway via JAK-STAT / 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 / PIP3 activates AKT signaling / MAPK cascade / cell-cell signaling / 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 MAPK cascade / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / signaling receptor complex / positive regulation of cell population proliferation / cell surface / Golgi apparatus / endoplasmic reticulum / 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 / 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 3
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.97 Å
AuthorsChen, X.J. / Liu, X.R. / Zhang, L.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)82202920 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 27, 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

Downloads & links

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Assembly

Deposited unit
A: Fibroblast growth factor receptor 3
B: Fibroblast growth factor receptor 3
C: Fibroblast growth factor receptor 3
D: Fibroblast growth factor receptor 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)134,07215
Polymers131,7444
Non-polymers2,32811
Water12,502694
1
A: Fibroblast growth factor receptor 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,5414
Polymers32,9361
Non-polymers6053
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area980 Å2
ΔGint-6 kcal/mol
Surface area13840 Å2
MethodPISA
2
B: Fibroblast growth factor receptor 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,4493
Polymers32,9361
Non-polymers5132
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area980 Å2
ΔGint-6 kcal/mol
Surface area13830 Å2
MethodPISA
3
C: Fibroblast growth factor receptor 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,5414
Polymers32,9361
Non-polymers6053
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area970 Å2
ΔGint-5 kcal/mol
Surface area13820 Å2
MethodPISA
4
D: Fibroblast growth factor receptor 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,5414
Polymers32,9361
Non-polymers6053
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1000 Å2
ΔGint-7 kcal/mol
Surface area13670 Å2
MethodPISA
Unit cell
Length a, b, c (Å)58.345, 112.843, 87.515
Angle α, β, γ (deg.)90.00, 94.93, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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


Mass: 32936.117 Da / Num. of mol.: 4
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-A1ESX / ~{N}-[1-methyl-3-[2-[[3-methyl-1-(2-morpholin-4-ylethyl)pyrazol-4-yl]amino]pyrimidin-4-yl]indol-6-yl]propanamide


Mass: 488.585 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Formula: C26H32N8O2 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 694 / 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: 2.18 Å3/Da / Density % sol: 43.54 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 25% (w/v) PEG 3350, 0.2 M MgCl2, and 0.1 M HEPES, pH 7.5

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Data collection

DiffractionMean temperature: 80 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL10U2 / Wavelength: 0.979183 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: 0.979183 Å / Relative weight: 1
ReflectionResolution: 1.97→112.9 Å / Num. obs: 79399 / % possible obs: 99.47 % / Redundancy: 5.8 % / CC1/2: 0.892 / Rmerge(I) obs: 0.2467 / Net I/σ(I): 5.29
Reflection shellResolution: 1.97→2.04 Å / Rmerge(I) obs: 0.9288 / Mean I/σ(I) obs: 1.84 / Num. unique obs: 7793 / CC1/2: 0.202

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Processing

Software
NameVersionClassification
PHENIX(1.19.2_4158: ???)refinement
DIALSdata reduction
EVAL15data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.97→19.1 Å / SU ML: 0.21 / Cross valid method: NONE / σ(F): 1.34 / Phase error: 23.45 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2368 3881 4.9 %
Rwork0.1873 --
obs0.1897 79249 99.59 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.97→19.1 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9037 0 166 694 9897
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0079454
X-RAY DIFFRACTIONf_angle_d1.06512785
X-RAY DIFFRACTIONf_dihedral_angle_d9.8271305
X-RAY DIFFRACTIONf_chiral_restr0.061399
X-RAY DIFFRACTIONf_plane_restr0.011620
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.97-1.990.29581420.25142526X-RAY DIFFRACTION94
1.99-2.020.29931420.23322695X-RAY DIFFRACTION99
2.02-2.050.25341360.22022654X-RAY DIFFRACTION100
2.05-2.070.30091300.23392689X-RAY DIFFRACTION99
2.07-2.10.27491480.2112684X-RAY DIFFRACTION100
2.1-2.130.2541610.20242635X-RAY DIFFRACTION100
2.13-2.170.29951470.20172716X-RAY DIFFRACTION100
2.17-2.20.25741270.1942675X-RAY DIFFRACTION100
2.2-2.240.2641460.19652714X-RAY DIFFRACTION100
2.24-2.280.26671470.20242629X-RAY DIFFRACTION99
2.28-2.330.26021340.18472707X-RAY DIFFRACTION100
2.33-2.370.25931610.18642673X-RAY DIFFRACTION100
2.37-2.420.27351240.19552745X-RAY DIFFRACTION100
2.42-2.480.27721370.19362651X-RAY DIFFRACTION100
2.48-2.540.28661340.19562736X-RAY DIFFRACTION100
2.54-2.610.27431370.19272675X-RAY DIFFRACTION100
2.61-2.690.23491470.22695X-RAY DIFFRACTION100
2.69-2.770.25051280.19172721X-RAY DIFFRACTION100
2.77-2.870.23981230.1932692X-RAY DIFFRACTION100
2.87-2.990.2591190.1892721X-RAY DIFFRACTION100
2.99-3.120.21771540.1872708X-RAY DIFFRACTION100
3.12-3.290.23261220.18082705X-RAY DIFFRACTION100
3.29-3.490.23141520.17462704X-RAY DIFFRACTION100
3.49-3.760.20531530.16912701X-RAY DIFFRACTION100
3.76-4.140.20331240.16192724X-RAY DIFFRACTION100
4.14-4.730.18251320.15432737X-RAY DIFFRACTION100
4.73-5.920.20631360.18452732X-RAY DIFFRACTION100
5.92-19.10.18291380.18122724X-RAY DIFFRACTION99

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