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- PDB-10oq: FGFR2 mutant D650V with compound 6 -

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Basic information

Entry
Database: PDB / ID: 10oq
TitleFGFR2 mutant D650V with compound 6
ComponentsFibroblast growth factor receptor 2
KeywordsTRANSFERASE / FGFR / FGFR2 / Fibroblast growth factor receptor / Tyrosine Kinase / Resistance Mutations / compound 6
Function / homology
Function and homology information


Signaling by FGFR2 amplification mutants / Signaling by FGFR2 fusions / fibroblast growth factor receptor signaling pathway involved in negative regulation of apoptotic process in bone marrow cell / fibroblast growth factor receptor signaling pathway involved in hemopoiesis / fibroblast growth factor receptor signaling pathway involved in positive regulation of cell proliferation in bone marrow / prostate epithelial cord arborization involved in prostate glandular acinus morphogenesis / lateral sprouting from an epithelium / mammary gland bud formation / branch elongation involved in salivary gland morphogenesis / mesenchymal cell differentiation involved in lung development ...Signaling by FGFR2 amplification mutants / Signaling by FGFR2 fusions / fibroblast growth factor receptor signaling pathway involved in negative regulation of apoptotic process in bone marrow cell / fibroblast growth factor receptor signaling pathway involved in hemopoiesis / fibroblast growth factor receptor signaling pathway involved in positive regulation of cell proliferation in bone marrow / prostate epithelial cord arborization involved in prostate glandular acinus morphogenesis / lateral sprouting from an epithelium / mammary gland bud formation / branch elongation involved in salivary gland morphogenesis / mesenchymal cell differentiation involved in lung development / fibroblast growth factor receptor signaling pathway involved in orbitofrontal cortex development / prostate gland morphogenesis / squamous basal epithelial stem cell differentiation involved in prostate gland acinus development / ventricular zone neuroblast division / lacrimal gland development / bud elongation involved in lung branching / otic vesicle formation / regulation of smooth muscle cell differentiation / prostate epithelial cord elongation / lung lobe morphogenesis / regulation of morphogenesis of a branching structure / epithelial cell proliferation involved in salivary gland morphogenesis / branching involved in labyrinthine layer morphogenesis / morphogenesis of embryonic epithelium / orbitofrontal cortex development / branching involved in salivary gland morphogenesis / mesenchymal cell proliferation involved in lung development / lung-associated mesenchyme development / epidermis morphogenesis / gland morphogenesis / branching morphogenesis of a nerve / embryonic organ morphogenesis / limb bud formation / endochondral bone growth / membranous septum morphogenesis / embryonic digestive tract morphogenesis / reproductive structure development / positive regulation of epithelial cell proliferation involved in lung morphogenesis / organ growth / branching involved in prostate gland morphogenesis / mesenchymal cell differentiation / FGFR2b ligand binding and activation / positive regulation of phospholipase activity / positive regulation of mesenchymal cell proliferation / FGFR2c ligand binding and activation / Activated point mutants of FGFR2 / Phospholipase C-mediated cascade; FGFR2 / embryonic cranial skeleton morphogenesis / regulation of osteoblast proliferation / lung alveolus development / embryonic pattern specification / fibroblast growth factor receptor activity / pyramidal neuron development / ureteric bud development / negative regulation of keratinocyte proliferation / outflow tract septum morphogenesis / regulation of smoothened signaling pathway / hair follicle morphogenesis / skeletal system morphogenesis / post-embryonic development / inner ear morphogenesis / mesodermal cell differentiation / digestive tract development / bone morphogenesis / odontogenesis / positive regulation of cell division / bone mineralization / midbrain development / embryonic organ development / Signaling by FGFR2 IIIa TM / regulation of osteoblast differentiation / ventricular cardiac muscle tissue morphogenesis / fibroblast growth factor receptor signaling pathway / PI-3K cascade:FGFR2 / cell fate commitment / positive regulation of cardiac muscle cell proliferation / lung development / cellular response to transforming growth factor beta stimulus / epithelial to mesenchymal transition / fibroblast growth factor binding / PI3K Cascade / regulation of ERK1 and ERK2 cascade / cellular response to retinoic acid / positive regulation of Wnt signaling pathway / positive regulation of vascular associated smooth muscle cell proliferation / SHC-mediated cascade:FGFR2 / axonogenesis / FRS-mediated FGFR2 signaling / animal organ morphogenesis / positive regulation of cell cycle / epithelial cell differentiation / Signaling by FGFR2 in disease / positive regulation of epithelial cell proliferation / peptidyl-tyrosine phosphorylation / in utero embryonic development / excitatory synapse / bone development / Negative regulation of FGFR2 signaling / receptor protein-tyrosine kinase / angiogenesis
Similarity search - Function
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. ...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 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.98 Å
AuthorsHoffman, I.D. / Nelson, K.J. / Bensen, D.C. / Rideout, M. / Hudkins, R.L. / Frye, C. / Bailey, J.B.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: J.Med.Chem. / Year: 2026
Title: Structure-Based Design of a Novel Covalent 4-(1-Methylindol-3-yl)pyrimidin-2-amine Series Targeting FGFR2 Resistance Mutations.
Authors: Hudkins, R.L. / Allen, E. / Iyer, S. / Balcer, A. / Neal, M. / Ye, Q. / Rideout, M. / Frye, C.B. / Nelson, K.J. / Hoffman, I.D. / Starrett, J.H. / Harris, T. / Swanson, R.V. / Bensen, D.C.
History
DepositionJan 29, 2026Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 15, 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 2
B: Fibroblast growth factor receptor 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)75,7009
Polymers74,2532
Non-polymers1,4467
Water1,17165
1
A: Fibroblast growth factor receptor 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,8945
Polymers37,1271
Non-polymers7674
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Fibroblast growth factor receptor 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,8064
Polymers37,1271
Non-polymers6793
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)96.743, 96.743, 145.622
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121

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Components

#1: Protein Fibroblast growth factor receptor 2 / FGFR-2 / K-sam / KGFR / Keratinocyte growth factor receptor


Mass: 37126.691 Da / Num. of mol.: 2 / Mutation: D650V
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: FGFR2, BEK, KGFR, KSAM / Production host: Escherichia coli (E. coli)
References: UniProt: P21802, receptor protein-tyrosine kinase
#2: Chemical ChemComp-A1C66 / N-[(3M)-3-{5-chloro-2-[4-(morpholin-4-yl)anilino]pyrimidin-4-yl}-1-methyl-1H-indol-6-yl]propanamide


Mass: 490.985 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C26H27ClN6O2
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 65 / 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: 2.65 Å3/Da / Density % sol: 53.57 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 5.6
Details: 22% PEG 4,000, 200 mM Ammonium Sulfate, 100 mM Sodium Citrate pH 5.6

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.97625 Å
DetectorType: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: Sep 16, 2025
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97625 Å / Relative weight: 1
ReflectionResolution: 1.98→54.966 Å / Num. obs: 55606 / % possible obs: 100 % / Redundancy: 20.6 % / CC1/2: 0.999 / Rmerge(I) obs: 0.188 / Net I/σ(I): 9.6
Reflection shellResolution: 1.98→2.01 Å / Redundancy: 19.5 % / Num. unique obs: 2700 / CC1/2: 0.329 / % possible all: 99.6

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Processing

Software
NameVersionClassification
REFMAC5.8.0430refinement
DIALSdata reduction
DIALSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.98→54.966 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.939 / SU B: 14.01 / SU ML: 0.17 / Cross valid method: FREE R-VALUE / ESU R: 0.157 / ESU R Free: 0.154 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.25144 2768 5 %RANDOM
Rwork0.20376 ---
obs0.20617 52790 99.92 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 51.256 Å2
Baniso -1Baniso -2Baniso -3
1-0.69 Å20.34 Å20 Å2
2--0.69 Å2-0 Å2
3----2.23 Å2
Refinement stepCycle: 1 / Resolution: 1.98→54.966 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4692 0 99 65 4856
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0124899
X-RAY DIFFRACTIONr_bond_other_d0.0010.0164696
X-RAY DIFFRACTIONr_angle_refined_deg2.71.8496619
X-RAY DIFFRACTIONr_angle_other_deg0.8621.7710866
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.4275587
X-RAY DIFFRACTIONr_dihedral_angle_2_deg18.581542
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.48610884
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.1220.2716
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.025641
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021051
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_it3.9932.7182357
X-RAY DIFFRACTIONr_mcbond_other3.9722.7192357
X-RAY DIFFRACTIONr_mcangle_it5.5734.8552938
X-RAY DIFFRACTIONr_mcangle_other5.5734.8562939
X-RAY DIFFRACTIONr_scbond_it6.0743.3262542
X-RAY DIFFRACTIONr_scbond_other5.8913.3162539
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other8.3095.7993675
X-RAY DIFFRACTIONr_long_range_B_refined9.65127.425398
X-RAY DIFFRACTIONr_long_range_B_other9.65727.425395
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.98→2.03 Å
RfactorNum. reflection% reflection
Rfree0.361 217 -
Rwork0.361 3802 -
obs--99.55 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
12.2718-0.5967-0.73721.79430.10181.70640.07860.0428-0.19130.111-0.05630.1510.0621-0.1781-0.02230.0693-0.0287-0.0450.02610.01180.266517.33789.433723.0083
23.2242-1.03110.16481.4997-0.68110.86940.09090.29160.0116-0.2414-0.161-0.16590.04060.26190.07010.06520.0012-0.00670.1440.00890.256946.116219.88144.8709
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A460 - 565
2X-RAY DIFFRACTION1A566 - 764
3X-RAY DIFFRACTION2B460 - 565
4X-RAY DIFFRACTION2B566 - 764

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