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- PDB-2i1m: cFMS tyrosine kinase (tie2 KID) in complex with an arylamide inhibitor -

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Basic information

Entry
Database: PDB / ID: 2i1m
TitlecFMS tyrosine kinase (tie2 KID) in complex with an arylamide inhibitor
ComponentsMacrophage colony-stimulating factor 1 receptor
KeywordsTRANSFERASE / Kinase Domain / Kinase Inhibitor Complex
Function / homology
Function and homology information


macrophage colony-stimulating factor receptor activity / forebrain neuron differentiation / CSF1-CSF1R complex / macrophage colony-stimulating factor signaling pathway / cell-cell junction maintenance / regulation of macrophage migration / cellular response to macrophage colony-stimulating factor stimulus / microglial cell proliferation / olfactory bulb development / mammary gland duct morphogenesis ...macrophage colony-stimulating factor receptor activity / forebrain neuron differentiation / CSF1-CSF1R complex / macrophage colony-stimulating factor signaling pathway / cell-cell junction maintenance / regulation of macrophage migration / cellular response to macrophage colony-stimulating factor stimulus / microglial cell proliferation / olfactory bulb development / mammary gland duct morphogenesis / positive regulation by host of viral process / ruffle organization / positive regulation of macrophage proliferation / regulation of bone resorption / positive regulation of cell motility / Other interleukin signaling / positive regulation of macrophage chemotaxis / cytokine binding / growth factor binding / cellular response to cytokine stimulus / monocyte differentiation / regulation of MAPK cascade / macrophage differentiation / hemopoiesis / positive regulation of protein tyrosine kinase activity / Transcriptional Regulation by VENTX / positive regulation of chemokine production / positive regulation of tyrosine phosphorylation of STAT protein / cell surface receptor protein tyrosine kinase signaling pathway / osteoclast differentiation / response to ischemia / regulation of actin cytoskeleton organization / axon guidance / receptor protein-tyrosine kinase / cytokine-mediated signaling pathway / peptidyl-tyrosine phosphorylation / Signaling by CSF1 (M-CSF) in myeloid cells / regulation of cell shape / protein phosphatase binding / protein tyrosine kinase activity / cell population proliferation / protein autophosphorylation / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / positive regulation of ERK1 and ERK2 cascade / receptor complex / positive regulation of cell migration / inflammatory response / positive regulation of protein phosphorylation / negative regulation of cell population proliferation / intracellular membrane-bounded organelle / innate immune response / positive regulation of cell population proliferation / negative regulation of apoptotic process / cell surface / signal transduction / protein homodimerization activity / nucleoplasm / ATP binding / plasma membrane
Similarity search - Function
Macrophage colony-stimulating factor 1 receptor / Tyrosine-protein kinase, receptor class III, conserved site / Receptor tyrosine kinase class III signature. / Immunoglobulin / Immunoglobulin domain / Immunoglobulin domain / Immunoglobulin subtype 2 / Immunoglobulin C-2 Type / Tyrosine-protein kinase, catalytic domain / Tyrosine kinase, catalytic domain ...Macrophage colony-stimulating factor 1 receptor / Tyrosine-protein kinase, receptor class III, conserved site / Receptor tyrosine kinase class III signature. / Immunoglobulin / Immunoglobulin domain / Immunoglobulin 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 / Phosphorylase Kinase; domain 1 / 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 / 2-Layer Sandwich / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Chem-5CN / Macrophage colony-stimulating factor 1 receptor
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsSchubert, C. / Schalk-Hihi, C.
CitationJournal: J.Biol.Chem. / Year: 2007
Title: Crystal structure of the tyrosine kinase domain of colony-stimulating factor-1 receptor (cFMS) in complex with two inhibitors.
Authors: Schubert, C. / Schalk-Hihi, C. / Struble, G.T. / Ma, H.C. / Petrounia, I.P. / Brandt, B. / Deckman, I.C. / Patch, R.J. / Player, M.R. / Spurlino, J.C. / Springer, B.A.
History
DepositionAug 14, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 28, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 23, 2017Group: Refinement description / Source and taxonomy / Category: entity_src_gen / software / Item: _software.name
Revision 1.4Oct 18, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.5Feb 21, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / 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
Remark 999SEQUENCE THE CLONE WAS TRIMMED TO RESIDUES 538-922 AND THE KINASE INSERT DOMAIN (RESIDUES 679-752) ...SEQUENCE THE CLONE WAS TRIMMED TO RESIDUES 538-922 AND THE KINASE INSERT DOMAIN (RESIDUES 679-752) WAS REPLACED WITH THE SEQUENCE OF THE KINASE INSERT DOMAIN FROM TIE2.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Macrophage colony-stimulating factor 1 receptor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,9522
Polymers37,6131
Non-polymers3391
Water3,171176
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)80.440, 80.440, 143.760
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number146
Space group name H-MH3

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Components

#1: Protein Macrophage colony-stimulating factor 1 receptor / cFMS Receptor Tyrosine Kinase / CSF-1-R / Fms proto-oncogene / c-fms / CD115 antigen


Mass: 37613.066 Da / Num. of mol.: 1 / Fragment: Kinase Domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CSF1R / Production host: Spodoptera frugiperda (fall armyworm)
References: UniProt: P07333, receptor protein-tyrosine kinase
#2: Chemical ChemComp-5CN / 5-CYANO-FURAN-2-CARBOXYLIC ACID [5-HYDROXYMETHYL-2-(4-METHYL-PIPERIDIN-1-YL)-PHENYL]-AMIDE


Mass: 339.388 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C19H21N3O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 176 / 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: 2.38 Å3/Da / Density % sol: 48.29 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5.2
Details: PEG 3350, sodium acetate, Li2SO4, pH 5.2, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: MACSCIENCE / Wavelength: 1.5418 Å
DetectorType: BRUKER SMART 6000 / Detector: CCD / Date: Sep 2, 2005 / Details: Osmic Blue
RadiationMonochromator: Osmic Blue / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.79→62.69 Å / Num. all: 30512 / Num. obs: 30512 / % possible obs: 94.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.1 % / Biso Wilson estimate: 14.2 Å2 / Limit h max: 38 / Limit h min: -38 / Limit k max: 44 / Limit k min: -38 / Limit l max: 79 / Limit l min: 0 / Observed criterion F max: 2634423.24 / Observed criterion F min: 7.5 / Rsym value: 0.0518 / Net I/σ(I): 9.4
Reflection shellResolution: 1.79→1.87 Å / Mean I/σ(I) obs: 1.7 / Rsym value: 0.388 / % possible all: 90.1

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Processing

Software
NameVersionClassificationNB
CNX2005refinement
PROTEUM PLUSdata collection
SAINTdata reduction
LSCALEdata scaling
CNX2002phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.8→62.69 Å / Rfactor Rfree error: 0.007 / Occupancy max: 1 / Occupancy min: 1 / Isotropic thermal model: Anisotropic / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.282 1510 5 %Random
Rwork0.237 ---
all0.25 32179 --
obs0.25 30454 94.6 %-
Solvent computationSolvent model: CNX bulk solvent model used / Bsol: 54.4444 Å2 / ksol: 0.368647 e/Å3
Displacement parametersBiso max: 93.33 Å2 / Biso mean: 36.24 Å2 / Biso min: 8.86 Å2
Baniso -1Baniso -2Baniso -3
1--3.36 Å2-0.88 Å20 Å2
2---3.36 Å20 Å2
3---6.73 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.31 Å0.26 Å
Luzzati d res low-5 Å
Luzzati sigma a0.46 Å0.4 Å
Luzzati d res high-1.8
Refinement stepCycle: LAST / Resolution: 1.8→62.69 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2469 0 25 176 2670
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.005
X-RAY DIFFRACTIONc_angle_deg1.2
X-RAY DIFFRACTIONc_dihedral_angle_d20.9
X-RAY DIFFRACTIONc_improper_angle_d0.75
LS refinement shell

Refine-ID: X-RAY DIFFRACTION

Resolution (Å)Rfactor RfreeNum. reflection Rfree% reflection Rfree (%)Rfactor RworkNum. reflection RworkRfactor Rfree errorNum. reflection allNum. reflection obs% reflection obs (%)
1.8-1.860.4651686.20.43925530.0363252272183.6
1.86-1.940.3831625.50.37527670.033195292991.6
1.94-2.030.33215150.30828650.0273243301693
2.03-2.130.3251304.30.26628900.0293210302094.1
2.13-2.270.2831625.30.2428690.0223208303194.5
2.27-2.440.3371645.30.25929480.0263235311296.2
2.44-2.690.28512540.23729860.0263224311196.5
2.69-3.080.29115750.23429620.0233203311997.3
3.08-3.880.24515950.20230200.0193224317998.6
3.88-62.690.2111324.10.19230840.0183221321699.8
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep_old.paramprotein_old.top
X-RAY DIFFRACTION2inh.paraminh.top
X-RAY DIFFRACTION3water_rep.paramwater.top

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