Citations in PubMed

Primary Citation PubMed: 17349580 Citations in PubMed

PDB ID Mentions in PubMed Central Article count: 5

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.

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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

Homology refinement successfully reconstructed the active crystallographic form of EGFR-L858R (pdb entry 2ITT) ( Figure 2A ).

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).

(A) Superposition of the crystal structures for the inactive EGFR-WT structure (initial structure in homology refinement) (pdb entry 2GS7, in green), EGFR-L858R mutant crystal structure (target structure in homology refinement) (pdb entry 2ITT, in blue) and computationally predicted EGFR-L858R model (in red).

(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


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


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

(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 b... st predicted mutant structures.

The predicted structural models and dynamics analysis of the L858R EGFR mutant conforms rather closely to the mutant X-ray structure (pdb entry 2ITT), moving considerably away from the initial wild type crystal structures and accurately reproducing the conformational rearrangement of the activation loop towards the active-like state ( Figure 8 ) [ 59 ].

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

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 V948... 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


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