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Yorodumi- PDB-5vo2: DLK in complex with inhibitor 5-(1-isopropyl-5-(1-(oxetan-3-yl)pi... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5vo2 | ||||||
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Title | DLK in complex with inhibitor 5-(1-isopropyl-5-(1-(oxetan-3-yl)piperidin-4-yl)-1H-pyrazol-3-yl)-3-(trifluoromethyl)pyridin-2-amine (compound 7) | ||||||
Components | Mitogen-activated protein kinase kinase kinase 12 | ||||||
Keywords | TRANSFERASE/TRANSFERASE Inhibitor / kinase / TRANSFERASE-TRANSFERASE Inhibitor complex | ||||||
Function / homology | Function and homology information mitogen-activated protein kinase kinase kinase / JUN kinase kinase kinase activity / negative regulation of motor neuron apoptotic process / positive regulation of protein kinase activity / positive regulation of JUN kinase activity / JNK cascade / protein serine/threonine kinase activator activity / post-translational protein modification / growth cone / peptidyl-serine phosphorylation ...mitogen-activated protein kinase kinase kinase / JUN kinase kinase kinase activity / negative regulation of motor neuron apoptotic process / positive regulation of protein kinase activity / positive regulation of JUN kinase activity / JNK cascade / protein serine/threonine kinase activator activity / post-translational protein modification / growth cone / peptidyl-serine phosphorylation / protein autophosphorylation / positive regulation of ERK1 and ERK2 cascade / protein kinase activity / intracellular signal transduction / protein phosphorylation / protein serine kinase activity / protein serine/threonine kinase activity / protein kinase binding / positive regulation of DNA-templated transcription / protein homodimerization activity / ATP binding / membrane / plasma membrane / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.96 Å | ||||||
Authors | HARRIS, S.F. / YIN, J. | ||||||
Citation | Journal: J. Med. Chem. / Year: 2017 Title: Selective Inhibitors of Dual Leucine Zipper Kinase (DLK, MAP3K12) with Activity in a Model of Alzheimer's Disease. Authors: Patel, S. / Meilandt, W.J. / Erickson, R.I. / Chen, J. / Deshmukh, G. / Estrada, A.A. / Fuji, R.N. / Gibbons, P. / Gustafson, A. / Harris, S.F. / Imperio, J. / Liu, W. / Liu, X. / Liu, Y. / ...Authors: Patel, S. / Meilandt, W.J. / Erickson, R.I. / Chen, J. / Deshmukh, G. / Estrada, A.A. / Fuji, R.N. / Gibbons, P. / Gustafson, A. / Harris, S.F. / Imperio, J. / Liu, W. / Liu, X. / Liu, Y. / Lyssikatos, J.P. / Ma, C. / Yin, J. / Lewcock, J.W. / Siu, M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5vo2.cif.gz | 71.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5vo2.ent.gz | 50 KB | Display | PDB format |
PDBx/mmJSON format | 5vo2.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5vo2_validation.pdf.gz | 686 KB | Display | wwPDB validaton report |
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Full document | 5vo2_full_validation.pdf.gz | 686.7 KB | Display | |
Data in XML | 5vo2_validation.xml.gz | 12 KB | Display | |
Data in CIF | 5vo2_validation.cif.gz | 15.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/vo/5vo2 ftp://data.pdbj.org/pub/pdb/validation_reports/vo/5vo2 | HTTPS FTP |
-Related structure data
Related structure data | 5vo1C 5cenS C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 34018.031 Da / Num. of mol.: 1 / Fragment: UNP residues 115-402 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: MAP3K12, ZPK / Production host: unidentified baculovirus References: UniProt: Q12852, mitogen-activated protein kinase kinase kinase |
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#2: Chemical | ChemComp-9FV / |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 1.93 Å3/Da / Density % sol: 36.31 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.7 / Details: 20% PEG 3350, 0.2 M Mg Acetate, 0.1 M Hepes pH 7.7 |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: SSRL / Beamline: BL7-1 / Wavelength: 1 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Aug 23, 2012 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.958→39.463 Å / Num. all: 5586 / Num. obs: 5586 / % possible obs: 99.5 % / Redundancy: 3.6 % / Biso Wilson estimate: 52.17 Å2 / Rpim(I) all: 0.071 / Rrim(I) all: 0.135 / Rsym value: 0.099 / Net I/av σ(I): 7.5 / Net I/σ(I): 11.5 / Num. measured all: 19858 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Phasing
Phasing | Method: molecular replacement |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5CEN Resolution: 2.96→35.79 Å / Cor.coef. Fo:Fc: 0.9094 / Cor.coef. Fo:Fc free: 0.7992 / Cross valid method: THROUGHOUT / σ(F): 0 / SU Rfree Blow DPI: 0.484
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Displacement parameters | Biso max: 113.07 Å2 / Biso mean: 34.14 Å2 / Biso min: 3 Å2
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Refine analyze | Luzzati coordinate error obs: 0.297 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.96→35.79 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.96→3.31 Å / Rfactor Rfree error: 0 / Total num. of bins used: 5
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