- PDB-4bfr: Discovery and Optimization of Pyrimidone Indoline Amide PI3Kbeta ... -
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Open data
ID or keywords:
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Basic information
Entry
Database: PDB / ID: 4bfr
Title
Discovery and Optimization of Pyrimidone Indoline Amide PI3Kbeta Inhibitors for the Treatment of Phosphatase and TENsin homologue (PTEN)-Deficient Cancers
Components
PHOSPHATIDYLINOSITOL 4,5-BISPHOSPHATE 3-KINASE CATALYTIC S SUBUNIT BETA ISOFORM
Keywords
TRANSFERASE / INHIBITOR
Function / homology
Function and homology information
IRS-mediated signalling / Signaling by ALK / negative regulation of hypoxia-induced intrinsic apoptotic signaling pathway / Tie2 Signaling / PI3K/AKT activation / PI3K Cascade / Role of LAT2/NTAL/LAB on calcium mobilization / Downstream signal transduction / GPVI-mediated activation cascade / negative regulation of sprouting angiogenesis ...IRS-mediated signalling / Signaling by ALK / negative regulation of hypoxia-induced intrinsic apoptotic signaling pathway / Tie2 Signaling / PI3K/AKT activation / PI3K Cascade / Role of LAT2/NTAL/LAB on calcium mobilization / Downstream signal transduction / GPVI-mediated activation cascade / negative regulation of sprouting angiogenesis / Role of phospholipids in phagocytosis / negative regulation of vascular endothelial growth factor signaling pathway / Erythropoietin activates Phosphoinositide-3-kinase (PI3K) / RAF/MAP kinase cascade / Interleukin receptor SHC signaling / Synthesis of PIPs at the plasma membrane / PIP3 activates AKT signaling / Downstream TCR signaling / Regulation of signaling by CBL / regulation of cell-matrix adhesion / positive regulation of neutrophil apoptotic process / PI5P, PP2A and IER3 Regulate PI3K/AKT Signaling / Interleukin-3, Interleukin-5 and GM-CSF signaling / RET signaling / embryonic cleavage / angiogenesis involved in wound healing / VEGFA-VEGFR2 Pathway / sphingosine-1-phosphate receptor signaling pathway / phosphatidylinositol 3-kinase complex, class IA / phosphatidylinositol 3-kinase complex / endothelial cell proliferation / 1-phosphatidylinositol-4-phosphate 3-kinase activity / 1-phosphatidylinositol-4,5-bisphosphate 3-kinase activity / DAP12 signaling / phosphatidylinositol-4,5-bisphosphate 3-kinase / phosphatidylinositol-3-phosphate biosynthetic process / negative regulation of MAPK cascade / 1-phosphatidylinositol-3-kinase activity / positive regulation of Rac protein signal transduction / homophilic cell adhesion via plasma membrane adhesion molecules / phosphatidylinositol-mediated signaling / phosphatidylinositol phosphate biosynthetic process / insulin receptor substrate binding / negative regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / positive regulation of endothelial cell migration / phosphatidylinositol 3-kinase/protein kinase B signal transduction / response to ischemia / brush border membrane / platelet activation / autophagy / intracellular calcium ion homeostasis / endocytosis / positive regulation of nitric oxide biosynthetic process / cell migration / kinase activity / midbody / non-specific serine/threonine protein kinase / phosphorylation / protein serine kinase activity / positive regulation of gene expression / nucleolus / nucleoplasm / ATP binding / nucleus / plasma membrane / cytoplasm / cytosol Similarity search - Function
Resolution: 2.8→56 Å / Cor.coef. Fo:Fc: 0.8932 / Cor.coef. Fo:Fc free: 0.8782 / SU R Cruickshank DPI: 1.126 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 1.012 / SU Rfree Blow DPI: 0.356 / SU Rfree Cruickshank DPI: 0.366 Details: IDEAL-DIST CONTACT TERM CONTACT SETUP. ALL ATOMS HAVE CCP4 ATOM TYPE FROM LIBRARY
Rfactor
Num. reflection
% reflection
Selection details
Rfree
0.275
3084
5.07 %
RANDOM
Rwork
0.26
-
-
-
obs
-
60840
99.74 %
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Displacement parameters
Biso mean: 76.87 Å2
Baniso -1
Baniso -2
Baniso -3
1-
-12.9221 Å2
0 Å2
0 Å2
2-
-
4.8927 Å2
0 Å2
3-
-
-
8.0294 Å2
Refine analyze
Luzzati coordinate error obs: 0.55 Å
Refinement step
Cycle: LAST / Resolution: 2.8→56 Å
Protein
Nucleic acid
Ligand
Solvent
Total
Num. atoms
13645
0
52
80
13777
Refine LS restraints
Refine-ID
Type
Dev ideal
Number
Restraint function
Weight
X-RAY DIFFRACTION
t_bond_d
0.008
13984
HARMONIC
2
X-RAY DIFFRACTION
t_angle_deg
0.87
18893
HARMONIC
2
X-RAY DIFFRACTION
t_dihedral_angle_d
4982
SINUSOIDAL
2
X-RAY DIFFRACTION
t_incorr_chiral_ct
X-RAY DIFFRACTION
t_pseud_angle
X-RAY DIFFRACTION
t_trig_c_planes
368
HARMONIC
2
X-RAY DIFFRACTION
t_gen_planes
1994
HARMONIC
5
X-RAY DIFFRACTION
t_it
13984
HARMONIC
20
X-RAY DIFFRACTION
t_nbd
X-RAY DIFFRACTION
t_omega_torsion
1.44
X-RAY DIFFRACTION
t_other_torsion
19.85
X-RAY DIFFRACTION
t_improper_torsion
X-RAY DIFFRACTION
t_chiral_improper_torsion
1764
SEMIHARMONIC
5
X-RAY DIFFRACTION
t_sum_occupancies
X-RAY DIFFRACTION
t_utility_distance
X-RAY DIFFRACTION
t_utility_angle
X-RAY DIFFRACTION
t_utility_torsion
X-RAY DIFFRACTION
t_ideal_dist_contact
15492
SEMIHARMONIC
4
LS refinement shell
Resolution: 2.8→2.87 Å / Total num. of bins used: 20
Rfactor
Num. reflection
% reflection
Rfree
0.2983
249
5.59 %
Rwork
0.2497
4209
-
all
0.2523
4458
-
obs
-
-
99.74 %
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