[English] 日本語
Yorodumi- PDB-2vo7: Structure of PKA complexed with 4-(4-Chlorobenzyl)-1-(7H-pyrrolo(... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2vo7 | ||||||
---|---|---|---|---|---|---|---|
Title | Structure of PKA complexed with 4-(4-Chlorobenzyl)-1-(7H-pyrrolo(2,3- d)pyrimidin-4-yl)piperidin-4-ylamine | ||||||
Components |
| ||||||
Keywords | TRANSFERASE / LIPOPROTEIN / ATP-BINDING / PHOSPHOPROTEIN / SERINE/THREONINE-PROTEIN KINASE / NUCLEOTIDE-BINDING / PROTEIN KINASE INHIBITOR / CAMP / KINASE / NUCLEUS / MYRISTATE / CYTOPLASM | ||||||
Function / homology | Function and homology information 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 / negative regulation of cAMP-dependent protein kinase activity / 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 / Mitochondrial protein degradation / cAMP-dependent protein kinase complex / Glucagon-like Peptide-1 (GLP1) regulates insulin secretion / AMP-activated protein kinase activity / negative regulation of protein import into nucleus / Vasopressin regulates renal water homeostasis via Aquaporins / protein kinase A regulatory subunit binding / protein kinase A catalytic subunit binding / mesoderm formation / sperm flagellum / negative regulation of TORC1 signaling / protein kinase A signaling / regulation of G2/M transition of mitotic cell cycle / 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 / negative regulation of transcription by RNA polymerase II / mitochondrion / ATP binding / nucleus / plasma membrane / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | BOS TAURUS (cattle) HOMO SAPIENS (human) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.98 Å | ||||||
Authors | Caldwell, J.J. / Davies, T.G. / Donald, A. / McHardy, T. / Rowlands, M.G. / Aherne, G.W. / Hunter, L.K. / Taylor, K. / Ruddle, R. / Raynaud, F.I. ...Caldwell, J.J. / Davies, T.G. / Donald, A. / McHardy, T. / Rowlands, M.G. / Aherne, G.W. / Hunter, L.K. / Taylor, K. / Ruddle, R. / Raynaud, F.I. / Verdonk, M. / Workman, P. / Garrett, M.D. / Collins, I. | ||||||
Citation | Journal: J.Med.Chem. / Year: 2008 Title: Identification of 4-(4-Aminopiperidin-1-Yl)-7H-Pyrrolo[2,3-D]Pyrimidines as Selective Inhibitors of Protein Kinase B Through Fragment Elaboration. Authors: Caldwell, J.J. / Davies, T.G. / Donald, A. / Mchardy, T. / Rowlands, M.G. / Aherne, G.W. / Hunter, L.K. / Taylor, K. / Ruddle, R. / Raynaud, F.I. / Verdonk, M. / Workman, P. / Garrett, M.D. / Collins, I. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 2vo7.cif.gz | 93.4 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb2vo7.ent.gz | 75.4 KB | Display | PDB format |
PDBx/mmJSON format | 2vo7.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/vo/2vo7 ftp://data.pdbj.org/pub/pdb/validation_reports/vo/2vo7 | HTTPS FTP |
---|
-Related structure data
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 40837.609 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) BOS TAURUS (cattle) / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: P00517, cAMP-dependent protein kinase | ||
---|---|---|---|
#2: Protein/peptide | Mass: 2226.411 Da / Num. of mol.: 1 / Fragment: RESIDUES 6-25 / Source method: obtained synthetically / Source: (synth.) HOMO SAPIENS (human) / References: UniProt: P61925 | ||
#3: Chemical | #4: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
---|
-Sample preparation
Crystal | Density Matthews: 2.33 Å3/Da / Density % sol: 46.89 % / Description: NONE |
---|
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RUH3R / Wavelength: 1.5418 |
Detector | Type: RIGAKU CCD / Detector: CCD |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.98→33 Å / Num. obs: 28363 / % possible obs: 95.9 % / Redundancy: 2.5 % / Rmerge(I) obs: 0.04 |
Reflection shell | Resolution: 1.98→2.1 Å / Rmerge(I) obs: 0.19 / Mean I/σ(I) obs: 4.2 / % possible all: 86.9 |
-Processing
Software | Name: REFMAC / Version: 5.2.0019I / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.98→33.36 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.922 / SU B: 3.771 / SU ML: 0.109 / Cross valid method: THROUGHOUT / ESU R: 0.181 / ESU R Free: 0.169 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. BROKEN DENSITY FOR PHE 54 OF THE GLYCINE LOOP. SOME INDICATIONS OF ALTERNATIVE CONFORMATIONS WERE PRESENT FOR THIS REGION BUT WERE POORLY ...Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. BROKEN DENSITY FOR PHE 54 OF THE GLYCINE LOOP. SOME INDICATIONS OF ALTERNATIVE CONFORMATIONS WERE PRESENT FOR THIS REGION BUT WERE POORLY DEFINED. ONLY THE DOMINANT CONFORMATION HAS BEEN BUILT.
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 22 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.98→33.36 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
|