Primary Citation PubMed: 11090628
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Structural evolution of the protein kinase-like superfamily.
(2005) PLoS Comput Biol 1
PubMed: 16244704 | PubMedCentral: PMC1261164 | DOI: 10.1371/journal.pcbi.0010049
Accession Numbers The Protein Data Bank ( http://www.rcsb.org/pdb/ ) accession numbers for proteins discussed in this paper are AFK (1CJA), APH(3′)-IIIa, (1J7U), ChaK (1IA9), CKA-2 (1NW1), Pak... (1F3M), PI3K (1E8X), PIPKIIβ (1BO1), and PKA (1CDK).
Publication Year: 2005
Multipolar representation of protein structure.
(2006) BMC Bioinformatics 7
PubMed: 16674828 | PubMedCentral: PMC1483839 | DOI: 10.1186/1471-2105-7-242
The subset contains nine structures: 1bol, 1ia9, 1e8x, 1cja, 1nwl, 1j7u, 1cdk, 1csn and 1ir3.
Publication Year: 2006
AcsD catalyzes enantioselective citrate desymmetrization in siderophore biosynthesis.
(2009) Nat Chem Biol 5
PubMed: 19182782 | PubMedCentral: PMC2644304 | DOI: 10.1038/nchembio.145
Carbons in this ATP are colored in magenta and taken from a superposition of phosphoinositide 3-kinase 1E8X 18 .
Publication Year: 2009
Emerging common themes in regulation of PIKKs and PI3Ks.
(2009) EMBO J 28
PubMed: 19779456 | PubMedCentral: PMC2752028 | DOI: 10.1038/emboj.2009.281
Figure 2 Superimposition of the FATC domain of S. cerevisiae Tor1 (PDB file 1w1n) and of helices αK12 and αK13 of the PI3K catalytic subunit p110γ (PDB file 1e8x) on the three-... imensional structure of the helical and kinase domains (KDs) of the PI3K catalytic subunit p110α (PDB file 2rd0), according to the alignment shown in Figure 1B .
Activating mutations in TOR are in similar structures as oncogenic mutations in PI3KCalpha.
(2009) ACS Chem Biol 4
PubMed: 19902965 | PubMedCentral: PMC2796128 | DOI: 10.1021/cb900193e
The template was PI3KCγ (RCSB, PDB 1e8x).
ATP Binding to TOR Residues in TOR equivalent to residues for ATP binding in PI3KCγ ( 1 ) are shown in relation to ATP and two Lu 3+ ions from the 1e8x template ( 3 ).
The structural elements are drawn from 1e8x and color-coded according to a scheme used throughout for TOR domains ( 99 ): FAT, sky blue; FRB, green, CAT, red; FIT (see text for domain definition), cyan; portion of the FATC, magenta.
We used ATP in PI3KCγ (1e8x) to approximate a starting position for Ku-0063794 for docking experiments with PI3KCγ and TOR.
We first placed S2 bound to human PI3KCγ (3ene) into the reference coordinates of our template porcine PI3KCγ (1e8x).
Coloring of PI3KCγ (1e8x): blue, helical domain; yellow, catalytic domain.
Magic Fit in DeepView was used for superposition of chains to place structure 3ene in the 1e8x reference.
Crystal structure of DNA-PKcs reveals a large open-ring cradle comprised of HEAT repeats.
(2010) Nature 463
PubMed: 20023628 | PubMedCentral: PMC2811870 | DOI: 10.1038/nature08648
Close visual inspection of the electron density maps in the area of kinase domain revealed a set of 3 helices the orientation of which was similar to that of catalytic domain of PI3Kγ kinase 2... (PDB accession code: 1e8x).
The catalytic domain of DNA-PKcs was built based on the crystal structure of PI3Kγ kinase (PDB accession code: 1e8x).
Publication Year: 2010
A new protein binding pocket similarity measure based on comparison of clouds of atoms in 3D: application to ligand prediction.
(2010) BMC Bioinformatics 11
PubMed: 20175916 | PubMedCentral: PMC2838872 | DOI: 10.1186/1471-2105-11-99
C) Positively charged protein regions around ATP molecules of PDB: 1E8X in grey and PDB: 1DV2 in red.
Similarly, the hydrophobic region interacting with the adenine ring of ATP in PDB: 1E8X and involving residues W812, I831, I879, I881, V882, A885, M953, F961, and I963 is equivalent to the hydrophobic region involving residues V131, V156, I157, L204, L278, I287, I437 in the superposed PDB: 1DV2 structure.
For example, the biotin carboxylase from E. coli (452 residues in PDB: 1DV2 ), and the phosphoinositide 3-kinase (961 residues in PDB: 1E8X ) are unrelated proteins.
D) Protein hydrophobic patches around ATP molecules of PDB: 1E8X in grey and PDB: 1DV2 in red.
Figure 4 shows the alignment of the two pockets, extracted from PDB: 1E8X and PDB: 1DV2 as clouds of atoms, and superposed by sup-CK .
A) overall structures of pdb: PDB: 1E8X in grey and PDB: 1DV2 in red superposed according to their binding sites using Sup-CK.
In particular, N951 and K807 interact with the γ phosphate of ATP in PDB: 1E8X and are found close respectively to K288 and H236 that play the same role in PDB: 1DV2 .
In the Result Section, we showed the example of the PDB: 1E8X and PDB: 1DV2 unrelated structures, binding ATP in similar conformations, and whose pockets were correctly superposed by the sup-CK method.
B) Superposition of the ATP molecules from PDB: 1DV2 and PDB: 1E8X when their binding sites are superposed.
We also observe that, K833 interacting with the β and α phosphates of ATP in PDB: 1E8X , is found close to K116 in PDB: 1DV2 after pockets superposition.
The p110 delta structure: mechanisms for selectivity and potency of new PI(3)K inhibitors.
(2010) Nat Chem Biol 6
PubMed: 20081827 | PubMedCentral: PMC2880452 | DOI: 10.1038/nchembio.293
For panel ( d ), the structure of the p110γ/ATP complex (PDB entry 1e8x) was superimposed on the C α -backbone of p110δ to show the proximity of the sulfonyl group of AS5 to th... alpha phosphate group of ATP (purple).
Structural biology of DNA repair: spatial organisation of the multicomponent complexes of nonhomologous end joining.
(2010) J Nucleic Acids 2010
PubMed: 20862368 | PubMedCentral: PMC2938450 | DOI: 10.4061/2010/621695
The modelling of DNA-PKcs catalytic domain was based on the crystal structure of one of its family members, the PI(3)K γ kinase (PDB code: 1E8X).
Regulation of lipid binding underlies the activation mechanism of class IA PI3-kinases.
(2012) Oncogene 31
PubMed: 22120714 | PubMedCentral: PMC3378484 | DOI: 10.1038/onc.2011.532
Positions of PS, IP3 and ATP are derived from the following structures: 1dsy ( Verdaguer et al., 1999 ), 1w2c ( Gonzalez et al., 2004 ) and 1e8x ( Walker et al., 1999 ).
Publication Year: 2012
Inhibitory effect of mTOR activator MHY1485 on autophagy: suppression of lysosomal fusion.
(2012) PLoS One 7
PubMed: 22927967 | PubMedCentral: PMC3425474 | DOI: 10.1371/journal.pone.0043418
The homologue structure used for mTOR modeling was the X-ray crystallography structure of PI3K (Phosphoinositide 3-kinase) (PDB ID: 1E8X).
Because mTOR had low sequence identity (18%) with the template structure (1E8X), the Z-score of the predicted model was −4.8.
A novel strategy for mechanism based computational drug discovery.
(2010) Biomark Cancer 2
PubMed: 24179383 | PubMedCentral: PMC3783289 | DOI: 10.4137/BIC.S3720
Docking Analysis In order to examine the effect of DADS against the kinases, their structures [1I8I (crystal structure of Mutant EGFR VIII), 1E8X (crystal structure of PI3K) and 1TVO (crystal structur... of ERK)] obtained from PDB ( www.rcsb.org ) were docked with the inhibitor, Diallyl Disulfide (DADS) ( Fig. 7 ).
Piceatannol suppresses the metastatic potential of MCF10A human breast epithelial cells harboring mutated H-ras by inhibiting MMP-2 expression.
(2013) Int J Mol Med 32
PubMed: 23877152 | PubMedCentral: PMC3812238 | DOI: 10.3892/ijmm.2013.1449
Molecular modeling Insight II (Accelrys, Inc., San Diego, CA, USA) was used for molecular docking and structure analysis; the crystal coordinates of PI3K in the complex with ATP (accession code 1E8X) ... re available on the Protein Data Bank ( http://www.rcsb.org/pdb/ ).
Publication Year: 2013
Molecular insights into the membrane-associated phosphatidylinositol 4-kinase II?.
(2014) Nat Commun 5
PubMed: 24675427 | PubMedCentral: PMC3974213 | DOI: 10.1038/ncomms4552
The root mean square deviation of aligned coordinates between the catalytic domains of PI4KIIα and PI3Kα (p110α, PDB code, 2RD0), PI3Kβ (p110β, PDB code, 2Y3A),... PI3Kγ (p110γ, PDB code, 1E8X), PI3Kδ (p110δ, PDB code, 2WXF), Vps34 (PDB code, 2X6H) and PIP4KIIβ (PDB code, 1BO1) are 3.08 Å, 3.18 Å, 3.50 Å, 2.89 Å, 3.60 Å and 3.82 Å, respectively.
Publication Year: 2014
Structural basis of nSH2 regulation and lipid binding in PI3K?.
(2014) Oncotarget 5
PubMed: 25105564 | PubMedCentral: PMC4170646 | DOI: 10.18632/oncotarget.2263
Catalysis and nSH2 domain inhibition The position of the bound ATP was modeled using a structural alignment of the PIP2 bound structure (PDB ID 4OVV) with the p110γ crystal structure in comple... with ATP (PDB ID 1E8X) (Fig.
(A) The relationship between the two substrates was inferred by modeling a molecule of ATP into the binding site (from the alignment with the p110γ-ATP complex structure, PDB ID 1E8X).
PubMed ID is not available.
Published in 2015
The ATP was placed in the PI3Kδ binding site by superimposing (using the “align” command in PyMOL) the structure of PI3Kγ bound with ATP (accession code 1E8X) ( 35 ).
Publication Year: 2015
Molecular Modeling The crystal coordinates of PI3K (PDB entry 1E8X), B-Raf (PDB entry 3C4E), and MEK1 (PDB entry 1S9J) were used for the docking of licochalcone A. Insight II (Accelrys Inc, San Diego,... CA, USA) was used for the modeling study and structure analysis.
Panel ( B ) shows the superposition of the model of the ligand docked into catalytic site to ATP crystallized PI3K (PDB ID: 1E8X).
The docked ligand (WYE) is in white, the ATP complexed into 1E8X in green, the BYM complexed into 2A4Z in Cyan.
In Figure 7B , we present the docked ligand superposed at ATP into the catalytic site for two crystal structures of PI3K (1E8X and 2A4Z).
Table 1 Ligands used as tool to assess 3D model of mTOR (protein name phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform) Ligands ID PDB Receptor ID PDB Resolution (Å) JZY 3L17 3.00 JZX 3L16 2.90 BYM 2A4Z 2.90 LXX 3L54 2.30 QJZ 3QJZ 2.90 JZW 3L13 a 3.00 OTZ 4FHJ 2.60 WYE 3LJ3 2.43 WYF 3MJW 2.87 ATP 1E8X 2.20 Note: a 3L13 is the template used to generate the model.
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