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- PDB-4v04: FGFR1 in complex with ponatinib. -

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Basic information

Entry
Database: PDB / ID: 4v04
TitleFGFR1 in complex with ponatinib.
ComponentsFIBROBLAST GROWTH FACTOR RECEPTOR 1 (FMS-RELATED TYROSINE KINASE 2, PFEIFFER SYNDROME), ISOFORM CRA_B
KeywordsTRANSFERASE
Function / homology
Function and homology information


fibroblast growth factor receptor activity / cytoplasmic vesicle / protein phosphorylation / ATP binding / cytosol
Similarity search - Function
Fibroblast growth factor receptor 1, catalytic domain / Tyrosine-protein kinase, catalytic domain / Tyrosine kinase, catalytic domain / Tyrosine protein kinases specific active-site signature. / Tyrosine-protein kinase, active site / Protein tyrosine and serine/threonine kinase / Serine-threonine/tyrosine-protein kinase, catalytic domain / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); domain 1 / Phosphorylase Kinase; domain 1 ...Fibroblast growth factor receptor 1, catalytic domain / Tyrosine-protein kinase, catalytic domain / Tyrosine kinase, catalytic domain / Tyrosine protein kinases specific active-site signature. / Tyrosine-protein kinase, active site / Protein tyrosine and serine/threonine kinase / Serine-threonine/tyrosine-protein kinase, catalytic domain / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); domain 1 / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; domain 1 / Protein kinase, ATP binding site / Protein kinases ATP-binding region signature. / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily / 2-Layer Sandwich / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Chem-0LI / Fibroblast growth factor receptor 1 (Fms-related tyrosine kinase 2, Pfeiffer syndrome), isoform CRA_b
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / OTHER / Resolution: 2.12 Å
AuthorsTucker, J. / Klein, T. / Breed, J. / Breeze, A. / Overman, R. / Phillips, C. / Norman, R.A.
CitationJournal: Structure / Year: 2014
Title: Structural Insights Into Fgfr Kinase Isoform Selectivity: Diverse Binding Modes of Azd4547 and Ponatinib in Complex with Fgfr1 and Fgfr4
Authors: Tucker, J.A. / Klein, T. / Breed, J. / Breeze, A.L. / Overman, R. / Phillips, C. / Norman, R.A.
History
DepositionSep 10, 2014Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 10, 2014Provider: repository / Type: Initial release
Revision 1.1Dec 17, 2014Group: Database references
Revision 1.2Apr 4, 2018Group: Data collection / Category: diffrn_source / Item: _diffrn_source.type
Revision 1.3May 8, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / entity / pdbx_database_status / pdbx_entity_nonpoly / struct_site
Item: _chem_comp.name / _database_2.pdbx_DOI ..._chem_comp.name / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity.pdbx_description / _pdbx_database_status.status_code_sf / _pdbx_entity_nonpoly.name / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: FIBROBLAST GROWTH FACTOR RECEPTOR 1 (FMS-RELATED TYROSINE KINASE 2, PFEIFFER SYNDROME), ISOFORM CRA_B
B: FIBROBLAST GROWTH FACTOR RECEPTOR 1 (FMS-RELATED TYROSINE KINASE 2, PFEIFFER SYNDROME), ISOFORM CRA_B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)72,49920
Polymers70,2712
Non-polymers2,22818
Water7,566420
1
A: FIBROBLAST GROWTH FACTOR RECEPTOR 1 (FMS-RELATED TYROSINE KINASE 2, PFEIFFER SYNDROME), ISOFORM CRA_B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,42512
Polymers35,1351
Non-polymers1,28911
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: FIBROBLAST GROWTH FACTOR RECEPTOR 1 (FMS-RELATED TYROSINE KINASE 2, PFEIFFER SYNDROME), ISOFORM CRA_B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,0748
Polymers35,1351
Non-polymers9397
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)207.255, 58.090, 65.231
Angle α, β, γ (deg.)90.00, 107.38, 90.00
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (-0.9942, 0.1076, -0.0032), (0.0892, 0.84, 0.535), (0.06022, 0.532, -0.8448)
Vector: 114.6, -13.84, 27.05)

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Components

#1: Protein FIBROBLAST GROWTH FACTOR RECEPTOR 1 (FMS-RELATED TYROSINE KINASE 2, PFEIFFER SYNDROME), ISOFORM CRA_B / FGFR1


Mass: 35135.340 Da / Num. of mol.: 2 / Fragment: KINASE, UNP RESIDUES 22-359 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: D3DSX2
#2: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical ChemComp-0LI / 3-(imidazo[1,2-b]pyridazin-3-ylethynyl)-4-methyl-N-{4-[(4-methylpiperazin-1-yl)methyl]-3-(trifluoromethyl)phenyl}benzam ide / Ponatinib / Ponatinib


Mass: 532.559 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C29H27F3N6O / Comment: medication*YM
#4: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


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


Mass: 18.015 Da / Num. of mol.: 420 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.67 Å3/Da / Density % sol: 53.87 % / Description: NONE
Crystal growDetails: 18-20% (W/V) PEG 8000, 200MM AMMONIUM SULPHATE, 100MM PCTP PH6.75, 20% (V/V) ETHYLENE GLYCOL

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E / Wavelength: 1.5418
DetectorType: RIGAKU CCD / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.12→98 Å / Num. obs: 41149 / % possible obs: 97 % / Observed criterion σ(I): 1 / Redundancy: 3.5 % / Biso Wilson estimate: 41.45 Å2 / Rmerge(I) obs: 0.04

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Processing

SoftwareName: BUSTER / Version: 2.11.5 / Classification: refinement
RefinementMethod to determine structure: OTHER
Starting model: NONE

Resolution: 2.12→21.37 Å / Cor.coef. Fo:Fc: 0.9508 / Cor.coef. Fo:Fc free: 0.93 / SU R Cruickshank DPI: 0.199 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.208 / SU Rfree Blow DPI: 0.174 / SU Rfree Cruickshank DPI: 0.172
RfactorNum. reflection% reflectionSelection details
Rfree0.228 2076 5.07 %RANDOM
Rwork0.186 ---
obs0.1881 40981 97.61 %-
Displacement parametersBiso mean: 50.52 Å2
Baniso -1Baniso -2Baniso -3
1-5.922 Å20 Å21.679 Å2
2---10.2249 Å20 Å2
3---4.3028 Å2
Refine analyzeLuzzati coordinate error obs: 0.29 Å
Refinement stepCycle: LAST / Resolution: 2.12→21.37 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4508 0 147 420 5075
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.014834HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.056546HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d1650SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes110HARMONIC2
X-RAY DIFFRACTIONt_gen_planes706HARMONIC5
X-RAY DIFFRACTIONt_it4834HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion3.09
X-RAY DIFFRACTIONt_other_torsion16.54
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion600SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies12HARMONIC1
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact5885SEMIHARMONIC4
LS refinement shellResolution: 2.12→2.17 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.2878 126 5.06 %
Rwork0.2264 2365 -
all0.2295 2491 -
obs--97.61 %
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)
12.2977-0.0351-0.37730.3464-0.25930.94590.06310.21950.1539-0.02680.0012-0.0146-0.1090.0201-0.0642-0.1013-0.0084-0.02830.010.0293-0.1379.5339-2.917617.6095
23.3509-1.18660.41461.03580.26111.07590.21580.4581-0.22350.0836-0.30640.12350.16350.04570.0906-0.08790.0062-0.0218-0.0437-0.0147-0.150633.96381.713213.8247

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