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- PDB-4v01: FGFR1 in complex with ponatinib (co-crystallisation). -

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Basic information

Entry
Database: PDB / ID: 4v01
TitleFGFR1 in complex with ponatinib (co-crystallisation).
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 / Resolution: 2.33 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 1.1Jul 22, 2015Group: Database references
Revision 1.2Apr 4, 2018Group: Data collection
Category: diffrn_radiation / diffrn_radiation_wavelength / diffrn_source
Item: _diffrn_radiation.pdbx_diffrn_protocol / _diffrn_radiation_wavelength.wavelength ..._diffrn_radiation.pdbx_diffrn_protocol / _diffrn_radiation_wavelength.wavelength / _diffrn_source.pdbx_wavelength_list / _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

Downloads & links

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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)72,53320
Polymers70,2712
Non-polymers2,26218
Water4,990277
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)36,1088
Polymers35,1351
Non-polymers9737
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
Components on special symmetry positions
IDModelComponents
11A-2028-

HOH

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Components

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


Mass: 35135.340 Da / Num. of mol.: 2 / Fragment: KINASE, UNP RESIDUES 22-329 / 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-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: SO4
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: C2H6O2
#4: 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


Mass: 532.559 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C29H27F3N6O / Comment: medication*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 277 / Source method: isolated from a natural source / Formula: H2O

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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: 2.67 Å3/Da / Density % sol: 53.87 %
Crystal growDetails: 20% PEG8000, 20MM AMMONIUM SULPHATE, 20% ETHYLENE GLYCOL, 100MM PCTP PH6.75

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E / Wavelength: 1.54 Å
DetectorType: SATURN 944 / Detector: CCD / Date: Jun 2, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2.33→98.89 Å / Num. obs: 30021 / % possible obs: 94.2 % / Redundancy: 2.3 % / Biso Wilson estimate: 46.2 Å2 / Rmerge(I) obs: 0.033 / Net I/σ(I): 18.2
Reflection shellResolution: 2.33→2.45 Å / Redundancy: 2.3 % / Rmerge(I) obs: 0.2 / Mean I/σ(I) obs: 5 / % possible all: 83.7

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Processing

Software
NameVersionClassification
BUSTER2.11.6refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementResolution: 2.33→98.89 Å / Cor.coef. Fo:Fc: 0.9416 / Cor.coef. Fo:Fc free: 0.9032 / SU R Cruickshank DPI: 0.294 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.304 / SU Rfree Blow DPI: 0.225 / SU Rfree Cruickshank DPI: 0.224
RfactorNum. reflection% reflectionSelection details
Rfree0.2378 1500 5.02 %RANDOM
Rwork0.1887 ---
obs0.1912 29865 93.42 %-
Displacement parametersBiso mean: 42.4 Å2
Baniso -1Baniso -2Baniso -3
1--1.5671 Å20 Å2-0.7902 Å2
2--3.0824 Å20 Å2
3----1.5152 Å2
Refine analyzeLuzzati coordinate error obs: 0.286 Å
Refinement stepCycle: LAST / Resolution: 2.33→98.89 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4265 0 148 277 4690
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.014538HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.036144HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d1577SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes99HARMONIC2
X-RAY DIFFRACTIONt_gen_planes704HARMONIC5
X-RAY DIFFRACTIONt_it4538HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion3
X-RAY DIFFRACTIONt_other_torsion17.36
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion568SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact5297SEMIHARMONIC4
LS refinement shellResolution: 2.33→2.41 Å / Total num. of bins used: 15
RfactorNum. reflection% reflection
Rfree0.2418 121 4.9 %
Rwork0.2053 2350 -
all0.2071 2471 -
obs--93.42 %
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)
12.1585-0.2052-0.28240.32310.04370.60720.09410.13520.1209-0.0719-0.05150.0278-0.06730.0404-0.04250.03480.0244-0.00190.05740.0148-0.021280.416-2.547418.4572
22.5239-0.8070.05090.85990.34960.85560.22220.295-0.2340.1063-0.22820.09250.0822-0.0620.0060.1430.0136-0.03190.099-0.02030.110534.21522.038813.617
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1{ A|465 - A|765 }
2X-RAY DIFFRACTION2{ B|461 - B|763 }

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