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- PDB-10oo: FGFR2 mutant D650V with compound 4 (AZD3463) -

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Basic information

Entry
Database: PDB / ID: 10oo
TitleFGFR2 mutant D650V with compound 4 (AZD3463)
ComponentsFibroblast growth factor receptor 2
KeywordsTRANSFERASE / FGFR2 / FGFR / Fibroblast growth factor receptor / Tyrosine Kinase / Resistance Mutations / AZD3463 / compound 4
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 / prostate gland morphogenesis / squamous basal epithelial stem cell differentiation involved in prostate gland acinus development / lacrimal gland development / otic vesicle formation / bud elongation involved in lung branching / 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 / orbitofrontal cortex development / morphogenesis of embryonic epithelium / branching involved in salivary gland morphogenesis / mesenchymal cell proliferation involved in lung development / lung-associated mesenchyme development / epidermis morphogenesis / branching morphogenesis of a nerve / gland morphogenesis / embryonic organ morphogenesis / limb bud formation / endochondral bone growth / membranous septum morphogenesis / reproductive structure development / embryonic digestive tract morphogenesis / positive regulation of epithelial cell proliferation involved in lung morphogenesis / organ growth / branching involved in prostate gland morphogenesis / mesenchymal cell differentiation / fibroblast growth factor receptor signaling pathway involved in orbitofrontal cortex development / ventricular zone neuroblast division / 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 / lung alveolus development / Phospholipase C-mediated cascade; FGFR2 / embryonic cranial skeleton morphogenesis / regulation of osteoblast proliferation / fibroblast growth factor receptor activity / embryonic pattern specification / 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 / inner ear morphogenesis / mesodermal cell differentiation / post-embryonic development / digestive tract development / bone morphogenesis / odontogenesis / bone mineralization / embryonic organ development / midbrain development / Signaling by FGFR2 IIIa TM / regulation of osteoblast differentiation / fibroblast growth factor receptor signaling pathway / ventricular cardiac muscle tissue morphogenesis / PI-3K cascade:FGFR2 / cell fate commitment / positive regulation of cardiac muscle cell proliferation / lung development / positive regulation of cell division / fibroblast growth factor binding / epithelial to mesenchymal transition / PI3K Cascade / cellular response to transforming growth factor beta stimulus / regulation of ERK1 and ERK2 cascade / positive regulation of Wnt signaling pathway / positive regulation of vascular associated smooth muscle cell proliferation / cellular response to retinoic acid / SHC-mediated cascade:FGFR2 / axonogenesis / FRS-mediated FGFR2 signaling / animal organ morphogenesis / epithelial cell differentiation / Signaling by FGFR2 in disease / positive regulation of epithelial cell proliferation / in utero embryonic development / peptidyl-tyrosine phosphorylation / positive regulation of cell cycle / excitatory synapse / Negative regulation of FGFR2 signaling / bone development / receptor protein-tyrosine kinase / Constitutive Signaling by Aberrant PI3K in Cancer
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: 1.85 Å
AuthorsHoffman, I.D. / Nelson, K.J.
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)75,72410
Polymers74,2532
Non-polymers1,4708
Water2,738152
1
A: Fibroblast growth factor receptor 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,8605
Polymers37,1271
Non-polymers7334
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Fibroblast growth factor receptor 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,8645
Polymers37,1271
Non-polymers7374
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)66.932, 77.985, 116.071
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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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-A1C65 / (4P)-N-[4-(4-aminopiperidin-1-yl)-2-methoxyphenyl]-5-chloro-4-(1H-indol-3-yl)pyrimidin-2-amine


Mass: 448.948 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C24H25ClN6O
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 5 / Source method: isolated from a natural source / Formula: SO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 152 / 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: 2.04 Å3/Da / Density % sol: 39.7 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 8.5
Details: 30% PEG 4,000, 200 mM Lithium Sulfate, 100 mM TRIS pH 8.5

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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: Aug 8, 2025
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97625 Å / Relative weight: 1
ReflectionResolution: 1.847→39.023 Å / Num. obs: 52406 / % possible obs: 99 % / Redundancy: 12.54 % / Rmerge(I) obs: 0.1627 / Net I/σ(I): 6.42
Reflection shellResolution: 1.85→1.95 Å / Redundancy: 11.85 % / Rmerge(I) obs: 0.8148 / Mean I/σ(I) obs: 1.36 / Num. unique obs: 7618 / % possible all: 96.9

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Processing

Software
NameVersionClassification
REFMAC5.8.0430refinement
SAINTdata reduction
SAINTdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.85→39.02 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.939 / SU B: 10.837 / SU ML: 0.149 / Cross valid method: FREE R-VALUE / ESU R: 0.156 / ESU R Free: 0.149 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.25576 2617 5 %RANDOM
Rwork0.21085 ---
obs0.21317 49641 98.82 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 35.715 Å2
Baniso -1Baniso -2Baniso -3
1--1.71 Å2-0 Å20 Å2
2--3.39 Å20 Å2
3----1.68 Å2
Refinement stepCycle: 1 / Resolution: 1.85→39.02 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4489 0 95 152 4736
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0124679
X-RAY DIFFRACTIONr_bond_other_d0.0010.0164521
X-RAY DIFFRACTIONr_angle_refined_deg2.2871.856321
X-RAY DIFFRACTIONr_angle_other_deg0.7581.77810440
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.7385555
X-RAY DIFFRACTIONr_dihedral_angle_2_deg12.176542
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.20410855
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.1140.2686
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.025382
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021018
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_it2.7382.0352238
X-RAY DIFFRACTIONr_mcbond_other2.7352.0342238
X-RAY DIFFRACTIONr_mcangle_it4.0773.632787
X-RAY DIFFRACTIONr_mcangle_other4.0793.6312788
X-RAY DIFFRACTIONr_scbond_it4.3292.5252441
X-RAY DIFFRACTIONr_scbond_other3.8062.4672422
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.6834.343505
X-RAY DIFFRACTIONr_long_range_B_refined8.01622.285239
X-RAY DIFFRACTIONr_long_range_B_other8.01622.135213
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.85→1.894 Å
RfactorNum. reflection% reflection
Rfree0.408 163 -
Rwork0.383 3481 -
obs--94.75 %
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)
10.90290.0221-0.0020.4704-0.05693.34120.0214-0.18870.07870.0599-0.01590.001-0.14380.0668-0.00540.067-0.0334-0.01140.0528-0.01440.0657-17.74812.8509-10.6066
21.47840.0584-0.1190.6045-0.40153.32410.0475-0.0761-0.07370.0368-0.0327-0.01570.0921-0.0315-0.01480.04080.0086-0.00780.0177-0.01240.0607-49.03313.832-24.8904
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A468 - 565
2X-RAY DIFFRACTION1A566 - 763
3X-RAY DIFFRACTION2B468 - 565
4X-RAY DIFFRACTION2B566 - 763

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