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- PDB-3zo4: The Synthesis and Evaluation of Diazaspirocyclic Protein Kinase I... -
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Open data
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Basic information
Entry | Database: PDB / ID: 3zo4 | ||||||
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Title | The Synthesis and Evaluation of Diazaspirocyclic Protein Kinase Inhibitors | ||||||
![]() | (CAMP-DEPENDENT PROTEIN KINASE ...) x 2 | ||||||
![]() | TRANSFERASE/INHIBITOR / TRANSFERASE-INHIBITOR COMPLEX | ||||||
Function / homology | ![]() CD209 (DC-SIGN) signaling / HDL assembly / Regulation of insulin secretion / Rap1 signalling / Ion homeostasis / PKA activation in glucagon signalling / DARPP-32 events / CREB1 phosphorylation through the activation of Adenylate Cyclase / GPER1 signaling / Factors involved in megakaryocyte development and platelet production ...CD209 (DC-SIGN) signaling / HDL assembly / Regulation of insulin secretion / Rap1 signalling / Ion homeostasis / PKA activation in glucagon signalling / DARPP-32 events / CREB1 phosphorylation through the activation of Adenylate Cyclase / GPER1 signaling / Factors involved in megakaryocyte development and platelet production / Loss of Nlp from mitotic centrosomes / Recruitment of mitotic centrosome proteins and complexes / Loss of proteins required for interphase microtubule organization from the centrosome / Anchoring of the basal body to the plasma membrane / AURKA Activation by TPX2 / RET signaling / Interleukin-3, Interleukin-5 and GM-CSF signaling / Recruitment of NuMA to mitotic centrosomes / VEGFA-VEGFR2 Pathway / PKA activation / GLI3 is processed to GLI3R by the proteasome / MAPK6/MAPK4 signaling / Regulation of PLK1 Activity at G2/M Transition / Hedgehog 'off' state / cAMP-dependent protein kinase inhibitor activity / cAMP-dependent protein kinase / cAMP-dependent protein kinase activity / cAMP-dependent protein kinase complex / AMP-activated protein kinase activity / Glucagon-like Peptide-1 (GLP1) regulates insulin secretion / Vasopressin regulates renal water homeostasis via Aquaporins / Mitochondrial protein degradation / protein kinase A regulatory subunit binding / mesoderm formation / sperm flagellum / negative regulation of TORC1 signaling / protein kinase A signaling / acrosomal vesicle / neuromuscular junction / cellular response to heat / peptidyl-serine phosphorylation / protein kinase activity / protein domain specific binding / protein phosphorylation / protein serine kinase activity / protein serine/threonine kinase activity / perinuclear region of cytoplasm / mitochondrion / ATP binding / nucleus / plasma membrane / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Allen, C.E. / Chow, C.L. / Caldwell, J.J. / Westwood, I.M. / van Montfort, R.L. / Collins, I. | ||||||
![]() | ![]() Title: Synthesis and evaluation of heteroaryl substituted diazaspirocycles as scaffolds to probe the ATP-binding site of protein kinases. Authors: Allen, C.E. / Chow, C.L. / Caldwell, J.J. / Westwood, I.M. / van Montfort, R.L. / Collins, I. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 171.7 KB | Display | ![]() |
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PDB format | ![]() | 133.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 3zo1C ![]() 3zo2C ![]() 3zo3C ![]() 2gfcS 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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1 |
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Unit cell |
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Components
-CAMP-DEPENDENT PROTEIN KINASE ... , 2 types, 2 molecules AI
#1: Protein | Mass: 40837.609 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
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#2: Protein/peptide | Mass: 2226.411 Da / Num. of mol.: 1 / Fragment: RESIDUES 6-25 / Source method: obtained synthetically / Source: (synth.) ![]() ![]() |
-Non-polymers , 5 types, 451 molecules ![](data/chem/img/MPD.gif)
![](data/chem/img/QWI.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/DMS.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/QWI.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/DMS.gif)
![](data/chem/img/HOH.gif)
#3: Chemical | ChemComp-MPD / ( |
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#4: Chemical | ChemComp-QWI / |
#5: Chemical | ChemComp-GOL / |
#6: Chemical | ChemComp-DMS / |
#7: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.73 Å3/Da / Density % sol: 54.9 % / Description: NONE |
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Crystal grow | Temperature: 277 K / pH: 6.5 Details: 25MM MES-BISTRIS PH6.5, 75MM LICL, 1MM DTT, 0.1MM EDTA, 1.5MM MEGA8; 4 DEGREES CELSIUS |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS / Detector: PIXEL / Date: Sep 29, 2012 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.92 Å / Relative weight: 1 |
Reflection | Resolution: 1.65→55.12 Å / Num. obs: 54405 / % possible obs: 99.7 % / Observed criterion σ(I): 1.5 / Redundancy: 4.4 % / Biso Wilson estimate: 26.35 Å2 / Rmerge(I) obs: 0.04 / Net I/σ(I): 20.7 |
Reflection shell | Resolution: 1.65→1.69 Å / Redundancy: 4.5 % / Rmerge(I) obs: 0.53 / Mean I/σ(I) obs: 2.7 / % possible all: 99.8 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 2GFC Resolution: 1.65→55.12 Å / Cor.coef. Fo:Fc: 0.9621 / Cor.coef. Fo:Fc free: 0.9576 / SU R Cruickshank DPI: 0.081 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.086 / SU Rfree Blow DPI: 0.084 / SU Rfree Cruickshank DPI: 0.081 Details: IDEAL-DIST CONTACT TERM CONTACT SETUP. ALL ATOMS HAVE CCP4 ATOM TYPE FROM LIBRARY.
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Displacement parameters | Biso mean: 29.36 Å2
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Refinement step | Cycle: LAST / Resolution: 1.65→55.12 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.65→1.69 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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