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- PDB-10ou: FGFR2 mutant D650V with compound 12 -

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Basic information

Entry
Database: PDB / ID: 10ou
TitleFGFR2 mutant D650V with compound 12
ComponentsFibroblast growth factor receptor 2
KeywordsTRANSFERASE / FGFR / FGFR2 / Fibroblast growth factor receptor / Tyrosine Kinase / Resistance Mutations / TYRX-0544
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 / lateral sprouting from an epithelium / mammary gland bud formation / branch elongation involved in salivary gland morphogenesis / mesenchymal cell differentiation involved in lung development / lacrimal gland 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 / lateral sprouting from an epithelium / mammary gland bud formation / branch elongation involved in salivary gland morphogenesis / mesenchymal cell differentiation involved in lung development / lacrimal gland development / prostate gland morphogenesis / otic vesicle formation / regulation of smooth muscle cell differentiation / regulation of morphogenesis of a branching structure / orbitofrontal cortex development / squamous basal epithelial stem cell differentiation involved in prostate gland acinus development / embryonic organ morphogenesis / branching morphogenesis of a nerve / morphogenesis of embryonic epithelium / endochondral bone growth / bud elongation involved in lung branching / epidermis morphogenesis / reproductive structure development / positive regulation of epithelial cell proliferation involved in lung morphogenesis / limb bud formation / gland morphogenesis / fibroblast growth factor receptor signaling pathway involved in orbitofrontal cortex development / ventricular zone neuroblast division / membranous septum morphogenesis / embryonic digestive tract morphogenesis / mesenchymal cell differentiation / positive regulation of phospholipase activity / epithelial cell proliferation involved in salivary gland morphogenesis / mesenchymal cell proliferation involved in lung development / FGFR2b ligand binding and activation / lung lobe morphogenesis / branching involved in prostate gland morphogenesis / branching involved in labyrinthine layer morphogenesis / FGFR2c ligand binding and activation / Activated point mutants of FGFR2 / Phospholipase C-mediated cascade; FGFR2 / regulation of osteoblast proliferation / fibroblast growth factor receptor activity / branching involved in salivary gland morphogenesis / embryonic cranial skeleton morphogenesis / lung-associated mesenchyme development / embryonic pattern specification / pyramidal neuron development / outflow tract septum morphogenesis / regulation of smoothened signaling pathway / mesodermal cell differentiation / bone morphogenesis / digestive tract development / positive regulation of mesenchymal cell proliferation / odontogenesis / ureteric bud development / organ growth / skeletal system morphogenesis / hair follicle morphogenesis / Signaling by FGFR2 IIIa TM / inner ear morphogenesis / lung alveolus development / prostate epithelial cord elongation / ventricular cardiac muscle tissue morphogenesis / regulation of osteoblast differentiation / prostate epithelial cord arborization involved in prostate glandular acinus morphogenesis / PI-3K cascade:FGFR2 / midbrain development / bone mineralization / positive regulation of cell division / fibroblast growth factor binding / fibroblast growth factor receptor signaling pathway / PI3K Cascade / epithelial to mesenchymal transition / negative regulation of keratinocyte proliferation / cell fate commitment / embryonic organ development / cellular response to transforming growth factor beta stimulus / regulation of ERK1 and ERK2 cascade / positive regulation of Wnt signaling pathway / positive regulation of cardiac muscle cell proliferation / SHC-mediated cascade:FGFR2 / positive regulation of vascular associated smooth muscle cell proliferation / cellular response to retinoic acid / FRS-mediated FGFR2 signaling / peptidyl-tyrosine phosphorylation / epithelial cell differentiation / positive regulation of cell cycle / Signaling by FGFR2 in disease / axonogenesis / lung development / excitatory synapse / positive regulation of epithelial cell proliferation / animal organ morphogenesis / post-embryonic development / Negative regulation of FGFR2 signaling / receptor protein-tyrosine kinase / bone development / Constitutive Signaling by Aberrant PI3K in Cancer / protein autophosphorylation
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: 1.77 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)78,36747
Polymers74,2532
Non-polymers4,11445
Water5,170287
1
A: Fibroblast growth factor receptor 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,04822
Polymers37,1271
Non-polymers1,92121
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Fibroblast growth factor receptor 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,32025
Polymers37,1271
Non-polymers2,19324
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)96.909, 96.909, 145.896
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121
Components on special symmetry positions
IDModelComponents
11B-912-

HOH

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Components

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Protein , 1 types, 2 molecules AB

#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

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Non-polymers , 5 types, 332 molecules

#2: Chemical ChemComp-A1C67 / N-[(3M)-3-{2-[(1-ethyl-1H-pyrazol-4-yl)amino]pyrimidin-4-yl}-1-methyl-1H-indol-6-yl]propanamide


Mass: 389.454 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H23N7O / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical...
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 22 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: SO4
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 287 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.66 Å3/Da / Density % sol: 53.82 %
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: ALS / Beamline: 8.3.1 / Wavelength: 0.97625 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: May 8, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97625 Å / Relative weight: 1
ReflectionResolution: 1.75→55.06 Å / Num. obs: 80528 / % possible obs: 99.9 % / Redundancy: 20.2 % / Rmerge(I) obs: 0.094 / Net I/σ(I): 15.4
Reflection shellResolution: 1.75→1.78 Å / Redundancy: 18.8 % / Rmerge(I) obs: 2.612 / Mean I/σ(I) obs: 1.5 / Num. unique obs: 4334 / % possible all: 98.7

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Processing

Software
NameVersionClassification
REFMAC5.8.0430refinement
SAINTdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.77→55.06 Å / Cor.coef. Fo:Fc: 0.971 / Cor.coef. Fo:Fc free: 0.956 / SU B: 4.58 / SU ML: 0.072 / Cross valid method: FREE R-VALUE / ESU R: 0.099 / ESU R Free: 0.103 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.2126 3894 5 %RANDOM
Rwork0.17178 ---
obs0.17384 73790 99.92 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 44.528 Å2
Baniso -1Baniso -2Baniso -3
1--0.4 Å2-0.2 Å2-0 Å2
2---0.4 Å20 Å2
3---1.29 Å2
Refinement stepCycle: 1 / Resolution: 1.77→55.06 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4818 0 263 287 5368
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0125176
X-RAY DIFFRACTIONr_bond_other_d0.0010.0164957
X-RAY DIFFRACTIONr_angle_refined_deg2.0971.8666947
X-RAY DIFFRACTIONr_angle_other_deg0.7251.77511490
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1655609
X-RAY DIFFRACTIONr_dihedral_angle_2_deg13.424541
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.06910913
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.1030.2754
X-RAY DIFFRACTIONr_gen_planes_refined0.010.025833
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021093
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_it3.212.7072421
X-RAY DIFFRACTIONr_mcbond_other3.2082.7082421
X-RAY DIFFRACTIONr_mcangle_it4.3094.8483023
X-RAY DIFFRACTIONr_mcangle_other4.3094.8493024
X-RAY DIFFRACTIONr_scbond_it5.5423.5332755
X-RAY DIFFRACTIONr_scbond_other5.5413.5342756
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other7.7856.1233921
X-RAY DIFFRACTIONr_long_range_B_refined9.95131.295689
X-RAY DIFFRACTIONr_long_range_B_other9.93931.25641
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.77→1.816 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.313 302 -
Rwork0.27 5318 -
obs--99.49 %
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)
11.3678-0.03720.12672.052-0.2991.18510.0301-0.0888-0.0156-0.00610.0321-0.19060.03820.1001-0.06220.0034-0.00750.00140.065-0.03170.0342-16.465510.3239-1.1928
20.9977-0.12340.43742.83050.46260.8933-0.07870.1220.1366-0.3457-0.02850.0949-0.2453-0.0430.10720.13380.0395-0.03220.0698-0.00650.0362-39.847530.2011-19.6929
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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