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- PDB-3c4f: FGFR TYROSINE KINASE DOMAIN IN COMPLEX WITH 3-(3-methoxybenzyl)-7... -

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Basic information

Entry
Database: PDB / ID: 3c4f
TitleFGFR TYROSINE KINASE DOMAIN IN COMPLEX WITH 3-(3-methoxybenzyl)-7-azaindole
ComponentsBasic fibroblast growth factor receptor 1
KeywordsTRANSFERASE / FIBROBLAST GROWTH FACTOR RECEPTOR / TYROSINE KINASE DOMAIN / RECEPTOR TYROSINE KINASE / FGFR1 / FGFR / Alternative splicing / ATP-binding / Chromosomal rearrangement / Disease mutation / Dwarfism / Glycoprotein / Heparin-binding / Immunoglobulin domain / Kallmann syndrome / Membrane / Nucleotide-binding / Phosphoprotein / Polymorphism / Transmembrane / Tyrosine-protein kinase
Function / homology
Function and homology information


Signaling by FGFR1 amplification mutants / negative regulation of fibroblast growth factor production / positive regulation of mitotic cell cycle DNA replication / regulation of extrinsic apoptotic signaling pathway in absence of ligand / Signaling by plasma membrane FGFR1 fusions / diphosphate metabolic process / FGFR1c and Klotho ligand binding and activation / vitamin D3 metabolic process / regulation of phosphate transport / regulation of lateral mesodermal cell fate specification ...Signaling by FGFR1 amplification mutants / negative regulation of fibroblast growth factor production / positive regulation of mitotic cell cycle DNA replication / regulation of extrinsic apoptotic signaling pathway in absence of ligand / Signaling by plasma membrane FGFR1 fusions / diphosphate metabolic process / FGFR1c and Klotho ligand binding and activation / vitamin D3 metabolic process / regulation of phosphate transport / regulation of lateral mesodermal cell fate specification / positive regulation of MAPKKK cascade by fibroblast growth factor receptor signaling pathway / cementum mineralization / positive regulation of endothelial cell chemotaxis to fibroblast growth factor / receptor-receptor interaction / response to sodium phosphate / regulation of branching involved in salivary gland morphogenesis by mesenchymal-epithelial signaling / fibroblast growth factor receptor signaling pathway involved in orbitofrontal cortex development / auditory receptor cell development / ventricular zone neuroblast division / Epithelial-Mesenchymal Transition (EMT) during gastrulation / positive regulation of parathyroid hormone secretion / chordate embryonic development / mesenchymal cell proliferation / paraxial mesoderm development / fibroblast growth factor receptor activity / FGFR1b ligand binding and activation / branching involved in salivary gland morphogenesis / Signaling by activated point mutants of FGFR1 / FGFR1c ligand binding and activation / organ induction / Downstream signaling of activated FGFR1 / Phospholipase C-mediated cascade: FGFR1 / positive regulation of phospholipase activity / lung-associated mesenchyme development / cell projection assembly / phosphatidylinositol-mediated signaling / outer ear morphogenesis / middle ear morphogenesis / embryonic limb morphogenesis / skeletal system morphogenesis / ureteric bud development / positive regulation of vascular endothelial cell proliferation / positive regulation of mesenchymal cell proliferation / cardiac muscle cell proliferation / inner ear morphogenesis / midbrain development / fibroblast growth factor binding / positive regulation of stem cell proliferation / Formation of paraxial mesoderm / regulation of cell differentiation / PI-3K cascade:FGFR1 / PI3K Cascade / epithelial to mesenchymal transition / positive regulation of blood vessel endothelial cell migration / fibroblast growth factor receptor signaling pathway / calcium ion homeostasis / chondrocyte differentiation / positive regulation of phospholipase C activity / SHC-mediated cascade:FGFR1 / cell maturation / positive regulation of cardiac muscle cell proliferation / FRS-mediated FGFR1 signaling / positive regulation of neuron differentiation / Signaling by FGFR1 in disease / SH2 domain binding / NCAM signaling for neurite out-growth / Signal transduction by L1 / skeletal system development / stem cell proliferation / stem cell differentiation / positive regulation of cell differentiation / sensory perception of sound / Negative regulation of FGFR1 signaling / neuron migration / positive regulation of MAP kinase activity / positive regulation of neuron projection development / receptor protein-tyrosine kinase / peptidyl-tyrosine phosphorylation / neuron projection development / cell surface receptor protein tyrosine kinase signaling pathway / Constitutive Signaling by Aberrant PI3K in Cancer / MAPK cascade / cell migration / PIP3 activates AKT signaling / heparin binding / gene expression / PI5P, PP2A and IER3 Regulate PI3K/AKT Signaling / cytoplasmic vesicle / RAF/MAP kinase cascade / angiogenesis / protein tyrosine kinase activity / in utero embryonic development / positive regulation of MAPK cascade / protein autophosphorylation / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / receptor complex / protein phosphorylation / positive regulation of cell population proliferation / negative regulation of transcription by RNA polymerase II / protein homodimerization activity
Similarity search - Function
Fibroblast growth factor receptor 1, catalytic domain / Fibroblast growth factor receptor family / Immunoglobulin / 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 ...Fibroblast growth factor receptor 1, catalytic domain / Fibroblast growth factor receptor family / Immunoglobulin / 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 / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); domain 1 / Phosphorylase Kinase; domain 1 / Ig-like domain profile. / Immunoglobulin-like domain / Phosphorylase Kinase; domain 1 / 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 / 2-Layer Sandwich / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
3-(3-methoxybenzyl)-1H-pyrrolo[2,3-b]pyridine / Fibroblast growth factor receptor 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.07 Å
AuthorsZhang, K.Y.J. / Wang, W.
CitationJournal: Proc.Natl.Acad.Sci.Usa / Year: 2008
Title: Discovery of a selective inhibitor of oncogenic B-Raf kinase with potent antimelanoma activity
Authors: Tsai, J. / Lee, J.T. / Wang, W. / Zhang, J. / Cho, H. / Mamo, S. / Bremer, R. / Gillette, S. / Kong, J. / Haass, N.K. / Sproesser, K. / Li, L. / Smalley, K.S. / Fong, D. / Zhu, Y.L. / ...Authors: Tsai, J. / Lee, J.T. / Wang, W. / Zhang, J. / Cho, H. / Mamo, S. / Bremer, R. / Gillette, S. / Kong, J. / Haass, N.K. / Sproesser, K. / Li, L. / Smalley, K.S. / Fong, D. / Zhu, Y.L. / Marimuthu, A. / Nguyen, H. / Lam, B. / Liu, J. / Cheung, I. / Rice, J. / Suzuki, Y. / Luu, C. / Settachatgul, C. / Shellooe, R. / Cantwell, J. / Kim, S.H. / Schlessinger, J. / Zhang, K.Y. / West, B.L. / Powell, B. / Habets, G. / Zhang, C. / Ibrahim, P.N. / Hirth, P. / Artis, D.R. / Herlyn, M. / Bollag, G.
History
DepositionJan 29, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 26, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 20, 2021Group: Database references / Derived calculations / Category: database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Feb 21, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Basic fibroblast growth factor receptor 1
B: Basic fibroblast growth factor receptor 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)69,4524
Polymers68,9752
Non-polymers4772
Water6,413356
1
A: Basic fibroblast growth factor receptor 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,7262
Polymers34,4881
Non-polymers2381
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Basic fibroblast growth factor receptor 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,7262
Polymers34,4881
Non-polymers2381
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
A: Basic fibroblast growth factor receptor 1
hetero molecules

A: Basic fibroblast growth factor receptor 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)69,4524
Polymers68,9752
Non-polymers4772
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area1670 Å2
MethodPISA
Unit cell
Length a, b, c (Å)208.190, 57.623, 65.368
Angle α, β, γ (deg.)90.00, 107.62, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Basic fibroblast growth factor receptor 1 / FGFR-1 / bFGF-R / Fms-like tyrosine kinase 2 / c-fgr / CD331 antigen


Mass: 34487.730 Da / Num. of mol.: 2 / Fragment: KINASE DOMAIN / Mutation: C488A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: FGFR1, FGFBR, FLG, FLT2 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)RIL
References: UniProt: P11362, receptor protein-tyrosine kinase
#2: Chemical ChemComp-C4F / 3-(3-methoxybenzyl)-1H-pyrrolo[2,3-b]pyridine


Mass: 238.284 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C15H14N2O
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 356 / 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: 2.71 Å3/Da / Density % sol: 54.59 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 16% PEG10k, 0.3M (NH4)2SO4, 5% Ethylene Glycol, 100 mM Bis-Tris pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 93 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1.1 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Jul 30, 2003
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 2.05→50 Å / Num. obs: 44044 / % possible obs: 95 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2 % / Rsym value: 0.103 / Net I/σ(I): 6.7
Reflection shellResolution: 2.05→2.16 Å / Redundancy: 2.1 % / Mean I/σ(I) obs: 1 / Num. unique all: 1914 / Rsym value: 0.793 / % possible all: 95

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Processing

Software
NameVersionClassification
REFMAC5.1.25refinement
Blu-Icedata collection
MOSFLMdata reduction
SCALAdata scaling
CCP4phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.07→50 Å / Cor.coef. Fo:Fc: 0.943 / Cor.coef. Fo:Fc free: 0.905 / SU B: 6.242 / SU ML: 0.159 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.224 / ESU R Free: 0.2 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.26436 2167 5.1 %RANDOM
Rwork0.21063 ---
obs0.2133 40646 94.52 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 30.094 Å2
Baniso -1Baniso -2Baniso -3
1--2.42 Å20 Å2-0.79 Å2
2--3.85 Å20 Å2
3----1.91 Å2
Refinement stepCycle: LAST / Resolution: 2.07→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4639 0 36 356 5031
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0224776
X-RAY DIFFRACTIONr_bond_other_d0.0020.024392
X-RAY DIFFRACTIONr_angle_refined_deg1.5921.9816450
X-RAY DIFFRACTIONr_angle_other_deg0.936310252
X-RAY DIFFRACTIONr_dihedral_angle_1_deg3.1965576
X-RAY DIFFRACTIONr_chiral_restr0.090.2702
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.025208
X-RAY DIFFRACTIONr_gen_planes_other0.0030.02924
X-RAY DIFFRACTIONr_nbd_refined0.1960.2989
X-RAY DIFFRACTIONr_nbd_other0.2270.24954
X-RAY DIFFRACTIONr_nbtor_other0.0840.22823
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.190.2291
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1940.220
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2730.2104
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1680.28
X-RAY DIFFRACTIONr_mcbond_it0.7291.52896
X-RAY DIFFRACTIONr_mcangle_it1.35424678
X-RAY DIFFRACTIONr_scbond_it1.91331880
X-RAY DIFFRACTIONr_scangle_it3.2134.51772
LS refinement shellResolution: 2.07→2.124 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.352 184
Rwork0.305 2939

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