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- PDB-2v4l: complex of human phosphoinositide 3-kinase catalytic subunit gamm... -
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Basic information
Entry | Database: PDB / ID: 2v4l | ||||||
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Title | complex of human phosphoinositide 3-kinase catalytic subunit gamma (p110 gamma) with PIK-284 | ||||||
![]() | PHOSPHATIDYLINOSITOL-4,5-BISPHOSPHATE 3-KINASE CATALYTIC SUBUNIT GAMMA ISOFORM | ||||||
![]() | TRANSFERASE / LIPID KINASE / PHOSPHOINOSITIDE / PYRAZOLOPYRIMIDINE / S1 / KINASE / PIK-284 / 3-KINASE / INHIBITOR / SIGNALING | ||||||
Function / homology | ![]() secretory granule localization / negative regulation of triglyceride catabolic process / natural killer cell chemotaxis / neutrophil extravasation / phosphatidylinositol-4-phosphate 3-kinase / positive regulation of acute inflammatory response / respiratory burst involved in defense response / negative regulation of cardiac muscle contraction / regulation of calcium ion transmembrane transport / T cell chemotaxis ...secretory granule localization / negative regulation of triglyceride catabolic process / natural killer cell chemotaxis / neutrophil extravasation / phosphatidylinositol-4-phosphate 3-kinase / positive regulation of acute inflammatory response / respiratory burst involved in defense response / negative regulation of cardiac muscle contraction / regulation of calcium ion transmembrane transport / T cell chemotaxis / negative regulation of fibroblast apoptotic process / phosphatidylinositol 3-kinase complex, class IB / sphingosine-1-phosphate receptor signaling pathway / phosphatidylinositol 3-kinase complex, class IA / dendritic cell chemotaxis / 1-phosphatidylinositol-4-phosphate 3-kinase activity / 1-phosphatidylinositol-4,5-bisphosphate 3-kinase activity / phosphatidylinositol-4,5-bisphosphate 3-kinase / phosphatidylinositol 3-kinase / phosphatidylinositol-3-phosphate biosynthetic process / 1-phosphatidylinositol-3-kinase activity / mast cell degranulation / Erythropoietin activates Phosphoinositide-3-kinase (PI3K) / hepatocyte apoptotic process / positive regulation of Rac protein signal transduction / Synthesis of PIPs at the plasma membrane / regulation of cell adhesion mediated by integrin / phosphatidylinositol-mediated signaling / phosphatidylinositol phosphate biosynthetic process / regulation of angiogenesis / T cell proliferation / cellular response to cAMP / GPVI-mediated activation cascade / T cell activation / neutrophil chemotaxis / ephrin receptor binding / phosphatidylinositol 3-kinase/protein kinase B signal transduction / positive regulation of endothelial cell migration / phosphorylation / positive regulation of cytokine production / positive regulation of MAP kinase activity / platelet aggregation / G beta:gamma signalling through PI3Kgamma / endocytosis / kinase activity / phospholipase C-activating G protein-coupled receptor signaling pathway / positive regulation of cytosolic calcium ion concentration / angiogenesis / adaptive immune response / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / non-specific serine/threonine protein kinase / protein kinase activity / inflammatory response / immune response / G protein-coupled receptor signaling pathway / innate immune response / protein serine kinase activity / protein serine/threonine kinase activity / ATP binding / identical protein binding / membrane / plasma membrane / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Apsel, B. / Gonzalez, B. / Blair, J.A. / Nazif, T.M. / Feldman, M.E. / Williams, R.L. / Shokat, K.M. / Knight, Z.A. | ||||||
![]() | ![]() Title: Targeted Polypharmacology: Discovery of Dual Inhibitors of Tyrosine and Phosphoinositide Kinases. Authors: Apsel, B. / Blair, J.A. / Gonzalez, B. / Nazif, T.M. / Feldman, M.E. / Aizenstein, B. / Hoffman, R. / Williams, R.L. / Shokat, K.M. / Knight, Z.A. | ||||||
History |
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Remark 700 | SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN ... SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED. |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 185.2 KB | Display | ![]() |
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PDB format | ![]() | 143.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 3en4C ![]() 3en5C ![]() 3en6C ![]() 3en7C ![]() 3eneC ![]() 2chxS S: Starting model for refinement C: citing same article ( |
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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: 110756.164 Da / Num. of mol.: 1 / Fragment: CATALYTIC SUBUNIT, RESIDUES 144-1102 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() References: UniProt: P48736, phosphatidylinositol-4,5-bisphosphate 3-kinase |
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#2: Chemical | ChemComp-ABJ / |
#3: Water | ChemComp-HOH / |
Nonpolymer details | 3-(4-AMINO-1-ISOPROPYL-1H-PYRAZOLO[3, 4-D]PYRIMIDIN-3-YL)PHENOL (284): THIS IS COMPOUND S1 IN THE ...3-(4-AMINO-1-ISOPROPYL-1H-PYRAZOLO[3, 4-D]PYRIMIDIN-3-YL)PHENOL (284): THIS IS COMPOUND S1 IN THE NAT CHEM BIOL PUBLICATIO |
Sequence details | RESIDUES 144-1102 |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.49 Å3/Da / Density % sol: 50 % / Description: NONE |
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Crystal grow | pH: 7.5 Details: RESERVOIR: 16-17% PEG 4000, 250 MM (NH4)2SO4 AND 100MM TRIS PH 7.5 PROTEIN: 4 MG/ML IN A BUFFER CONTAINING 0.5 MM (NH4)2SO4, 20 MM TRIS PH 7.2, 1% ETHYLENE GLYCOL, 0.02% CHAPS AND 5 MM DTT ...Details: RESERVOIR: 16-17% PEG 4000, 250 MM (NH4)2SO4 AND 100MM TRIS PH 7.5 PROTEIN: 4 MG/ML IN A BUFFER CONTAINING 0.5 MM (NH4)2SO4, 20 MM TRIS PH 7.2, 1% ETHYLENE GLYCOL, 0.02% CHAPS AND 5 MM DTT DROPS WERE 1MICROLITER PROTEIN PLUS 1 MICROLITER RESERVOIR |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC CCD / Detector: CCD / Date: Jan 5, 2005 / Details: TORROIDAL MIRROR |
Radiation | Monochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.934 Å / Relative weight: 1 |
Reflection | Resolution: 2.5→54.4 Å / Num. obs: 33672 / % possible obs: 99.7 % / Observed criterion σ(I): -3.7 / Redundancy: 3.7 % / Rmerge(I) obs: 0.05 / Net I/σ(I): 10 |
Reflection shell | Resolution: 2.5→2.64 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.32 / Mean I/σ(I) obs: 1.7 / % possible all: 97.4 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 2CHX Resolution: 2.5→54.39 Å / Cor.coef. Fo:Fc: 0.92 / Cor.coef. Fo:Fc free: 0.88 / SU B: 11.231 / SU ML: 0.257 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.681 / ESU R Free: 0.344 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 21.03 Å2
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Refinement step | Cycle: LAST / Resolution: 2.5→54.39 Å
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