Citations in PubMed

Primary Citation PubMed: 17349580 Citations in PubMed

PDB ID Mentions in PubMed Central Article count: 13

Citations in PubMed

This linkout lists citations, indexed by PubMed, to the Primary Citation for this PDB ID.

PDB ID Mentions in PubMed Central

Data mentions are occurrences of PDB IDs in the full text articles from the PubMedCentral Open Access Subset of currently about 1 million articles. For each article, the sentences containing the PDB ID are listed. Article titles can be filtered by keywords and sorted by year.

  • 3 per page
  • 5 per page
  • 10 per page
  • view all
  • Publication Year
  • Ascending
  • Descending

Hierarchical modeling of activation mechanisms in the ABL and EGFR kinase domains: thermodynamic and mechanistic catalysts of kinase activation by cancer mutations.

(2009) PLoS Comput Biol 5

PubMed: 19714203 | PubMedCentral: PMC2722018 | DOI: 10.1371/journal.pcbi.1000487

Materials and Methods Structure Preparation In simulations of the ABL and EGFR kinase domains, we used the following crystal structures from the Protein Data Bank (PDB): pdb entry 1IEP (inactive ABL s... ructure), pdb entry 2G1T (Src-like inactive ABL structure), pdb entry 1M52 (active ABL structure), pdb entry 1XKK (Src/Cdk-like inactive EGFR structure), pdb entry 2GS7 (Src/Cdk-like inactive EGFR structure) and pdb entry 2J6M (active EGFR structure).

The crystal structures of EGFR represent the following conformational forms: the Lapatinib-bound, inactive structure (pdb entry 1XKK) (A), the Src/Cdk-like inactive structure (pdb entry 2GS7) (B), and the active structure (pdb entry 2J6M) (C).

Similarly, TMD simulations were carried out for EGFR-WT, EGFR-T790M and EGFR-L858R to model conformational transitions between the Src/Cdk-like inactive form of EGFR (pdb entry 1XKK) and the target active EGFR form (pdb entry 2J6M for EGFR-WT; pdb entry 2JIU for EGFR-T790M; and pdb entry 2ITT for EGFR-L858R).

(B) A close-up comparison between activation loop conformations in the crystal structures of inactive EGFR-WT (pdb entry 2J6M, in green), EGFR-L858R mutant crystal structure (pdb entry 2ITT, in blue) and the predicted mutant conformation (in red).

Publication Year: 2009


Sequence and structure signatures of cancer mutation hotspots in protein kinases.

(2009) PLoS One 4

PubMed: 19834613 | PubMedCentral: PMC2759519 | DOI: 10.1371/journal.pone.0007485

(A) Structural localization of the conserved mutational hotspots is illustrated using the crystal structure of the active EGFR kinase (pdb entry 2J6M).

(B) Structural localization of cancer driver mutations with the high oncogenic potential is illustrated using the crystal structure of the active EGFR kinase (pdb entry 2J6M).

Publication Year: 2009


Drug discovery using chemical systems biology: weak inhibition of multiple kinases may contribute to the anti-cancer effect of nelfinavir.

(2011) PLoS Comput Biol 7

PubMed: 21552547 | PubMedCentral: PMC3084228 | DOI: 10.1371/journal.pcbi.1002037

The wheat cartoon represents the backbone structure of EGFR (PDB id: 2J6M).

An example is shown in Figure 3 for the case of epidermal growth factor receptor (EGFR) protein kinase domain (PDB id: 2J6M).

Publication Year: 2011


Computational modeling of allosteric communication reveals organizing principles of mutation-induced signaling in ABL and EGFR kinases.

(2011) PLoS Comput Biol 7

PubMed: 21998569 | PubMedCentral: PMC3188506 | DOI: 10.1371/journal.pcbi.1002179

Allosteric Signatures of Mutation-Induced EGFR Activation In this section, we analyzed allosteric signatures of the EGFR kinase catalytic domain using the results of MD simulations in the following fu... ctional states: the inactive EGFR form (PDB ID 1XKK) [77] ; the active EGFR form (PDB ID 2J6M) [78] , the active form of the EGFR-T790M mutant (PDB ID 2JIT) [79] .

Structural mapping of residues involved in long-range communication in different functional states of the EGFR catalytic domain: ( A ) the inactive EGFR-WT structure (PDB ID 1XKK); ( B ) the active EGFR-WT structure (PDB ID 2J6M); ( C ) the active form of the EGFR-T790M mutant (PDB ID 2JIT).

In MD simulations of the ABL and EGFR kinase domains, we used the following crystal structures : PDB ID 1IEP (inactive ABL structure) [70] , PDB ID 1M52 (active ABL structure) [71] , [72] , PDB ID 2G1T (Src-like inactive ABL structure) [109] , PDB ID 2Z60 (the active form of the ABL-T315I mutant) [75] , PDB ID 1XKK (Src/Cdk-like inactive EGFR structure) [77] , PDB ID 2GS7 (Src/Cdk-like inactive EGFR structure) [109] , and PDB ID 2J6M (active EGFR structure) [78] , and PDB ID 2JIT (EGFR-T790M mutant) [79] .

Publication Year: 2011


The energy landscape analysis of cancer mutations in protein kinases.

(2011) PLoS One 6

PubMed: 21998754 | PubMedCentral: PMC3188581 | DOI: 10.1371/journal.pone.0026071

A more extensive minimally frustrated network of interactions rigidifies the active form of the catalytic domain for ABL (PDB ID 1M52) [ 91] , [92 ] and EGFR (PDB ID 2J6M) [ 118 ] .

The analysis was performed using inhibitor-bound crystal structures of EGFR in the inactive form (PDB ID 1XKK) [ 117 ] and active form (PDB ID 2J6M) [ 118 ] .

The analysis was performed on the unbound form of the crystal structures of EGFR in the inactive form (PDB ID 1XKK) [ 117 ] and active form (PDB ID 2J6M) [ 118 ] .

The set of active kinase conformations included EGFR (PDB ID 2J6M), BTK (PDB ID 1K2P), and RET (PDB ID 2IVS).

The crystal structure of EGFR-WT in the active form (PDB ID 2J6M) [ 118 ] was used as a template for structural mapping.

The crystal structure of EGFR-WT in the active form (PDB ID 2J6M) [ 118 ] was used in this example of a comparative analysis.

Publication Year: 2011


Differential sensitivity of ERBB2 kinase domain mutations towards lapatinib.

(2011) PLoS One 6

PubMed: 22046346 | PubMedCentral: PMC3203921 | DOI: 10.1371/journal.pone.0026760

Crystal structures of complexes with erlotinib (1M17), lapatinib (1XKK, 3BBT), gefitinib (2ITY, 2ITO, 2ITZ), and AEE788 (2J6M, 2ITP, 2ITT, 2JIU), representing both active and inactive states of the ki... ase domain, were superimposed and inspected using the graphics program PyMOL ( www.pymol.org ) [14] , [16] , [23] – [25] .

Publication Year: 2011


Evaluating caveolin interactions: do proteins interact with the caveolin scaffolding domain through a widespread aromatic residue-rich motif?

(2012) PLoS One 7

PubMed: 23028656 | PubMedCentral: PMC3444507 | DOI: 10.1371/journal.pone.0044879

Figure S4 View of the context of the CBM of EGFR (A, PDB code 2J6M; [ 131 ] ), insulin receptor (B, PDB code 3BU3; [ 132 ] ) integrin-linked kinase (C, PDB code 3REP; Fukuda & Qin, to be publi... hed), PTEN (D, PDB code 1D5R; [ 133 ] ), Slo1 (E, PDB code 3MT5; [ 134 ] ), and the two CBMs of PDK1 (F and G, PDB code 1UU3; [ 135 ] ).

Publication Year: 2012


Coupled mutation finder: a new entropy-based method quantifying phylogenetic noise for the detection of compensatory mutations.

(2012) BMC Bioinformatics 13

PubMed: 22963049 | PubMedCentral: PMC3577461 | DOI: 10.1186/1471-2105-13-225

In this study, we analyzed human EGFR (pdb entry 2J6M) and GCK (pdb entry 1V4S) proteins with a false discovery rate ( FDR ) of 1%.

Figure 6 Four p -value distributions of (transformed) normalized mutual information values for human GCK and EFGR proteins having PDB-ID 1V4S and 2J6M, respectively.

Essential sites of human EGFR and GCK proteins To evaluate the CMF -significant residue sites, we have investigated essential sites of human EGFR (pdb entry 2J6M) and GCK (pdb entry 1V4S) proteins.

Figure 1 CMF -significant nsSNP positions in human EGFR protein (PDB-Entry 2J6M).

Figure 2 CMF -significant residue positions are in contact with gefitinib binding sites in human EGFR protein (PDB-Entry 2J6M).

Publication Year: 2012


Structure-functional prediction and analysis of cancer mutation effects in protein kinases.

(2014) Comput Math Methods Med 2014

PubMed: 24817905 | PubMedCentral: PMC4000980 | DOI: 10.1155/2014/653487

(b) The dynamics profile of the active wild-type EGFR (pdb id 2J6M) crystal structure of the wild-type EGFR.

We pursued structural modeling of L858R mutant starting from both inactive (pdb entries 1XKK, 2GS7) and active wild-type EGFR structures (pdb entries 2J6M, 2ITX, 2ITW, and 2ITY).

(c) A close-up comparison between conformations of the activation loop in the wild-type EGFR crystal structure (pdb entry 2J6M, green), L858R mutant crystal structure (pdb entry 2ITT, pink), and two best predicted mutant structures.

Publication Year: 2014


Structure-based ensemble-QSAR model: a novel approach to the study of the EGFR tyrosine kinase and its inhibitors.

(2014) Acta Pharmacol Sin 35

PubMed: 24335842 | PubMedCentral: PMC4076596 | DOI: 10.1038/aps.2013.148

According to our study, the co-crystallized ligands in 2J6M (2J6M_W) and 2JIU (2JIU_AW) are not similar to the docked molecules in clusters A and C, respectively, but the highest TPR 1% values were ob... ained for these clusters ( Figure 3 ).

Original PDB code Resolution (Å) Mutation Conformation (Inactive or active form) Re-compiled code 1M17 2.60   active 1M17 1M17_W 1XKK 2.40   inactive 1XKK 1XKK_W 2GS7 2.60 V948R inactive 2GS7_A 2GS7_AW         2GS7_B 2GS7_BW 2ITN 2.47 G719S active 2ITN 2ITN_W         2ITN_M 2ITN_WM 2ITO 3.25 G719S inactive 2ITO 2ITO_M 2ITP 2.74 G719S active 2ITP 2ITP_W         2ITP_M 2ITP_WM 2ITQ 2.68 G719S inactive 2ITQ 2ITQ_M 2ITT 2.73 L858R active 2ITT 2ITT_W         2ITT_M 2ITT_WM 2ITU 2.80 L858R active 2ITU 2ITU_W         2ITU_M 2ITU_WM 2ITV 2.47 L858R active 2ITV 2ITV_W         2ITV_M 2ITV_WM 2ITW 2.88   active 2ITW 2ITW_W 2ITX 2.98   active 2ITX   2ITY 3.42   active 2ITY 2ITY_W 2ITZ 2.80   active 2ITZ 2ITZ_W 2J6M 3.10   active 2J6M 2J6M_W 2JIU 3.05 T790M active 2JIU_A 2JIU_AW         2JIU_AM 2JIU_AWM 2RGP 2.00   inactive 2RGP 2RGP_W 3BEL 2.30   inactive 3BEL   3GT8 3.95 V948R inactive 3GT8_A 3GT8_B         3GT8_C 3GT8_D Each new code consists of two parts separated by an underscore.

Publication Year: 2014


Quantum coupled mutation finder: predicting functionally or structurally important sites in proteins using quantum Jensen-Shannon divergence and CUDA programming.

(2014) BMC Bioinformatics 15

PubMed: 24694117 | PubMedCentral: PMC4098773 | DOI: 10.1186/1471-2105-15-96

First, to test the functionality of QCMF-significant individual residue sites we analysed the essential sites of two human proteins: epidermal growth factor receptor (EGFR) (pdb entry 2J6M) and glucok... nase (GCK) (pdb entry 1V4S).

Using the example of the human EGFR protein (PDB-Entry 2J6M), Figure 6 illustrates that the method we developed in [ 5 ] to determine significant column pairs is well-applicable for both ℚ ent and ℚ sep .

Figure 1 QCMF-significant residue positions are in contact with catalytic residues in human EGFR protein (PDB-Entry 2J6M).

Figure 2 QCMF-significant residue positions are in contact with gefitinib binding sites in human EGFR protein (PDB-Entry 2J6M).

Figure 6 p-value distributions of ℚ ent and ℚ sep -values for human EGFR protein (PDB-Entry 2J6M).

Publication Year: 2014


Structure-based network analysis of activation mechanisms in the ErbB family of receptor tyrosine kinases: the regulatory spine residues are global mediators of structural stability and allosteric interactions.

(2014) PLoS One 9

PubMed: 25427151 | PubMedCentral: PMC4245119 | DOI: 10.1371/journal.pone.0113488

Structural similarities in the functional regions of the active EGFR-WT conformation (in blue), DFG-in/αC-helix-in (pdb id 2ITX, 2J6M); the active EGFR-L858R conformation (in red), DFG-in/�... 3b1;C-helix-in (pdb id 2ITV); and the active EGFR-T790M conformation (in green), DFG-in/αC-helix-in (pdb id 2JIT).

The active EGFR crystal structures used in simulations included the following pdb entries: pdb id 2GS2 (active, Apo EGFR-WT); pdb id 2ITX (active, EGFR-WT in complex with AMP-PNP); pdb id 2J6M (active, EGFR-WT in complex with AEE788 inhibitor); pdb id 2ITV (active, EGFR-WT in complex with AMP-PNP); and pdb id 2JIT (active, Apo EGFR-T790M).

Structural differences in the functional regions of the EGFR-WT crystal structures: Cdk/Src-IF1 state (in blue), DFG-in/αC-helix-out (pdb id 1XKK, 2GS7); Cdk/Src-IF2 conformation (in red), DFG-out/αC-helix-out (pdb id 2RF9); and the active conformation (in green), DFG-in/αC-helix-in (pdb id 2ITX, 2J6M).

Publication Year: 2014


PubMed ID is not available.

Published in 2015

PubMedCentral: PMC4517520

Table 2 General information about the mutations of the 42 HER family protein kinase domain PDB ID a TKI-sensitive TKI-resistant Protein conformation G719S LREA L858R T790M DFG-motif αC positio... (Å) b EGFR  4LQM − L––– + − DFG-in 7.690  4LRM − − − − DFG-in 8.028  4LL0 − − + + DFG-in 9.460  4LI5 − − − − DFG-in 8.266  4JQ7 − − − − DFG-in 8.843  4JQ8 − − − − DFG-in 8.071  4JR3 − − − DFG-in 7.903  4JRV − L––– − − DFG-in 7.929  3W32 − − − − DFG-out 12.717  3W33 − − − − DFG-out 12.846  3W2O − − + + DFG-in 8.065  3W2P − − + + DFG-in 8.109  3W2Q − − + + DFG-in 8.394  3W2R − − + + DFG-out 12.056  4I22 − LRKA + + DFG-out 12.384  4I23 − L––A − − DFG-in 7.750  4I24 − L––A − + DFG-out 12.399  4HJO − − − − DFG-out 12.327  4G5J − K––– − − DFG-in 7.807  4G5P − − − + DFG-in 8.786  3UG2 − –––– − + DFG-in 8.308  3POZ − LA–– − − DFG-out 12.430  3LZB − − − − DFG-out 11.673  3IKA − − − + DFG-in 9.314  2RGP − LR–K − − DFG-out 12.098  3BEL − − − − DFG-out 12.033  2JIU − − − + DFG-in 8.868  2JIV − − − + DFG-out-like 12.634  2ITO + − − − DFG-in 7.446  2ITP + − − − DFG-in 7.673  2ITT − − + − DFG-in 7.682  2ITY − − − − DFG-in 7.481  2ITZ − − + − DFG-in 7.717  2J6M − − − − DFG-in 7.647  2J5E − − − − DFG-in 7.394  2J5F − − − − DFG-in 7.642  1XKK − LREK − − DFG-out 11.967  1M17 − − − − DFG-in 8.037 HER2  3RCD − LR–– − − DFG-out 10.997 HER3  4OTW − IEDK L858V − DFG-out 13.635 HER4  2R4B − LN–– − − DFG-out 11.299  3BBT − LK–– − − DFG-out 12.537 Notes: a All the HER protein kinase crystal complexes collected from the PDB (up to 05/28/2014); b The distance between the αC carbon atoms of D xDFG.81 and E αC.24 .

Publication Year: 2015