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- PDB-5kmj: TrkA JM-kinase with {N}-(2-pyridylmethyl)-2-[2-(2-thienyl)indol-1... -
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Open data
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Basic information
Entry | Database: PDB / ID: 5kmj | ||||||
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Title | TrkA JM-kinase with {N}-(2-pyridylmethyl)-2-[2-(2-thienyl)indol-1-yl]acetamide | ||||||
![]() | High affinity nerve growth factor receptor | ||||||
![]() | TRANSFERASE/TRANSFERASE INHIBITOR / kinase / juxtamembrane / inhibitor / TRANSFERASE-TRANSFERASE INHIBITOR complex | ||||||
Function / homology | ![]() behavioral response to formalin induced pain / neurotrophin p75 receptor binding / olfactory nerve development / response to hydrostatic pressure / TRKA activation by NGF / PLC-gamma1 signalling / programmed cell death involved in cell development / Signalling to STAT3 / neurotrophin receptor activity / mechanoreceptor differentiation ...behavioral response to formalin induced pain / neurotrophin p75 receptor binding / olfactory nerve development / response to hydrostatic pressure / TRKA activation by NGF / PLC-gamma1 signalling / programmed cell death involved in cell development / Signalling to STAT3 / neurotrophin receptor activity / mechanoreceptor differentiation / nerve growth factor receptor activity / neurotrophin binding / Sertoli cell development / axonogenesis involved in innervation / GPI-linked ephrin receptor activity / nerve growth factor signaling pathway / Retrograde neurotrophin signalling / nerve growth factor binding / NGF-independant TRKA activation / sympathetic nervous system development / Signalling to p38 via RIT and RIN / ARMS-mediated activation / positive regulation of Ras protein signal transduction / positive regulation of programmed cell death / positive regulation of synapse assembly / PI3K/AKT activation / Frs2-mediated activation / regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / detection of temperature stimulus involved in sensory perception of pain / neurotrophin TRK receptor signaling pathway / response to axon injury / neuron development / Signalling to RAS / detection of mechanical stimulus involved in sensory perception of pain / response to electrical stimulus / peptidyl-tyrosine autophosphorylation / transmembrane receptor protein tyrosine kinase activity / positive regulation of synaptic transmission, glutamatergic / response to nutrient levels / B cell differentiation / cellular response to nerve growth factor stimulus / positive regulation of GTPase activity / axon guidance / receptor protein-tyrosine kinase / kinase binding / positive regulation of neuron projection development / cellular response to nicotine / circadian rhythm / peptidyl-tyrosine phosphorylation / recycling endosome membrane / positive regulation of angiogenesis / neuron projection development / late endosome / late endosome membrane / positive regulation of NF-kappaB transcription factor activity / early endosome membrane / protein tyrosine kinase activity / neuron apoptotic process / negative regulation of neuron apoptotic process / protein autophosphorylation / learning or memory / positive regulation of ERK1 and ERK2 cascade / early endosome / receptor complex / endosome membrane / response to xenobiotic stimulus / positive regulation of protein phosphorylation / negative regulation of cell population proliferation / axon / protein phosphorylation / neuronal cell body / dendrite / negative regulation of apoptotic process / cell surface / protein homodimerization activity / protein-containing complex / ATP binding / identical protein binding / plasma membrane Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Su, H.P. | ||||||
![]() | ![]() Title: Structural characterization of nonactive site, TrkA-selective kinase inhibitors. Authors: Su, H.P. / Rickert, K. / Burlein, C. / Narayan, K. / Bukhtiyarova, M. / Hurzy, D.M. / Stump, C.A. / Zhang, X. / Reid, J. / Krasowska-Zoladek, A. / Tummala, S. / Shipman, J.M. / Kornienko, M. ...Authors: Su, H.P. / Rickert, K. / Burlein, C. / Narayan, K. / Bukhtiyarova, M. / Hurzy, D.M. / Stump, C.A. / Zhang, X. / Reid, J. / Krasowska-Zoladek, A. / Tummala, S. / Shipman, J.M. / Kornienko, M. / Lemaire, P.A. / Krosky, D. / Heller, A. / Achab, A. / Chamberlin, C. / Saradjian, P. / Sauvagnat, B. / Yang, X. / Ziebell, M.R. / Nickbarg, E. / Sanders, J.M. / Bilodeau, M.T. / Carroll, S.S. / Lumb, K.J. / Soisson, S.M. / Henze, D.A. / Cooke, A.J. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 79.3 KB | Display | ![]() |
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PDB format | ![]() | 55.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 730 KB | Display | ![]() |
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Full document | ![]() | 730.7 KB | Display | |
Data in XML | ![]() | 13.1 KB | Display | |
Data in CIF | ![]() | 18 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5kmiC ![]() 5kmkC ![]() 5kmlC ![]() 5kmmC ![]() 5kmnC ![]() 5kmoC ![]() 4pmmS C: citing same article ( S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 37266.746 Da / Num. of mol.: 1 Fragment: catalytic domain with juxtamembrane region, UNP residues 376-698 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() References: UniProt: P04629, receptor protein-tyrosine kinase |
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#2: Chemical | ChemComp-6UF / ~{ |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.39 Å3/Da / Density % sol: 48.46 % / Mosaicity: 0 ° |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 50mM MES pH 6.5, 150 mM NaCl, 5mM TCEP, 0.1% beta-OctylGlucoside |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: ![]() ![]() ![]() | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 23, 2012 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.045→22.55 Å / Num. all: 22948 / Num. obs: 22948 / % possible obs: 100 % / Redundancy: 9.9 % / Biso Wilson estimate: 35.59 Å2 / Rpim(I) all: 0.026 / Rrim(I) all: 0.082 / Rsym value: 0.074 / Net I/av σ(I): 6.941 / Net I/σ(I): 18.7 / Num. measured all: 227022 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1 / Rejects: _
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 4PMM Resolution: 2.04→22.55 Å / Cor.coef. Fo:Fc: 0.9498 / Cor.coef. Fo:Fc free: 0.9292 / SU R Cruickshank DPI: 0.174 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.174 / SU Rfree Blow DPI: 0.151 / SU Rfree Cruickshank DPI: 0.152
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Displacement parameters | Biso max: 124.53 Å2 / Biso mean: 39.05 Å2 / Biso min: 13.81 Å2
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Refine analyze | Luzzati coordinate error obs: 0.257 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.04→22.55 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.04→2.14 Å / Total num. of bins used: 11
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