Citations in PubMed

Primary Citation PubMed: 17349580 Citations in PubMed

PDB ID Mentions in PubMed Central Article count: 16

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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CMASA: an accurate algorithm for detecting local protein structural similarity and its application to enzyme catalytic site annotation.

(2010) BMC Bioinformatics 11

PubMed: 20796320 | PubMedCentral: PMC2936402 | DOI: 10.1186/1471-2105-11-439

PINTS have its own website, so we used 2ity (a protein kinase) active sites to search PINTS SCOP_specials database (a database of PINTS, same as nrSCOP database in this work).

Publication Year: 2010


Identification of potent EGFR inhibitors from TCM Database@Taiwan.

(2011) PLoS Comput Biol 7

PubMed: 22022246 | PubMedCentral: PMC3192800 | DOI: 10.1371/journal.pcbi.1002189

EGFR Protein Sequence, Structure, and Characteristics The EGFR protein sequence (EGFR_HUMAN, P00533) used in this study was obtained from Swiss-Prot [50] , and the 3D structure (PDB: 2ITY) [51] used f... r analyses was downloaded from Protein Data Bank.

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


Identifying HER2 inhibitors from natural products database.

(2011) PLoS One 6

PubMed: 22174899 | PubMedCentral: PMC3236219 | DOI: 10.1371/journal.pone.0028793

Molecular Dynamics (MD) Simulation The HER2 protein structure used within this study was constructed through homology modeling using EGFR kinase domain structures found in Protein Data Bank (PDB: 2ITY... and 2J5E).

Publication Year: 2011


Structural and spectroscopic analysis of the kinase inhibitor bosutinib and an isomer of bosutinib binding to the Abl tyrosine kinase domain.

(2012) PLoS One 7

PubMed: 22493660 | PubMedCentral: PMC3320885 | DOI: 10.1371/journal.pone.0029828

For comparison, the binding modes of erlotinib (red) and gefitinib (pink) are also shown, and were obtained by aligning the structures of these compounds bound to EGFR (pdb codes 1M17 and 2ITY for erl... tinib and gefitinib, respectively) on the hinge region of Abl.

Publication Year: 2012


EGFR-targeted therapy for non-small cell lung cancer: focus on EGFR oncogenic mutation.

(2013) Int J Med Sci 10

PubMed: 23423768 | PubMedCentral: PMC3575628 | DOI: 10.7150/ijms.4609

(B) Ribbon diagram of wild-type human EGFR (PDB code 2ITY), illustrating binding of gefitinib to the active site of the kinase.

Publication Year: 2013


Design and Evaluation of Novel Antimicrobial and Anticancer Agents Among Tetrazolo[1,5-c]quinazoline-5-thione S-Derivatives.

(2013) Sci Pharm 81

PubMed: 23641327 | PubMedCentral: PMC3617672 | DOI: 10.3797/scipharm.1208-13

Docking, scoring, and visual inspection of synthesized substances into the ATP binding site of EGFR To help us understand the anticancer activity of the observed compounds and guide further SAR studie... , molecular docking of compounds 2.1 , 2.2 , 5.1–5.4 , 6.1 – 6.3, and 7.1 into the ATP binding site of EGFR (2ITY.

The crystal structure of the enzyme EGFR (2ITY.

Publication Year: 2013


From bench to bedside: lessons learned in translating preclinical studies in cancer drug development.

(2013) J Natl Cancer Inst 105

PubMed: 24052618 | PubMedCentral: PMC3787906 | DOI: 10.1093/jnci/djt209

Protein structures of the wild-type T790 (PDB code: 2ITY) and acquired mutation T790M (PDB code: 3UG2) are shown.

Publication Year: 2013


Personalized prediction of EGFR mutation-induced drug resistance in lung cancer.

(2013) Sci Rep 3

PubMed: 24092472 | PubMedCentral: PMC3790204 | DOI: 10.1038/srep02855

We isolate them from their bound complexes 2ITY and 1M17 downloaded from the Protein Data Bank (PDB) 16 .

Publication Year: 2013


Pathway analysis for drug repositioning based on public database mining.

(2014) J Chem Inf Model 54

PubMed: 24460210 | PubMedCentral: PMC3956470 | DOI: 10.1021/ci4005354

42 − 44 The crystal structure of the primary target of human EGFR in complex with gefitinib was retrieved from MMDB (PDB ID: 2ITY); 68 more protein targets (most of them are tyrosine kinases) ... ith moderate affinity to gefitinib were retrieved from the BioAssay database (Table 1 ).

Publication Year: 2014


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

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).

Publication Year: 2014


Exploration of type II binding mode: A privileged approach for kinase inhibitor focused drug discovery?

(2014) ACS Chem Biol 9

PubMed: 24730530 | PubMedCentral: PMC4068218 | DOI: 10.1021/cb500129t

(B) Gefitinib complexes with EGFR (PDB ID: 2ITY) in type I binding.

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: PMC4364680

With MatchMaker in UCSF Chimera [ 30 ], we aligned the optimized structure to the template complex “2ITY” (EGFR-gefitinib complex) or “1 M17” (EGFR-erlotinib co... plex) to obtain the mutant-drug complex.

Publication Year: 2015


PubMed ID is not available.

Published in 2015

PubMedCentral: PMC4439022

(a) and (b), The structures of gefitinib (PDB: 2ITY), with its atoms and essential pharmacophore (quinazoline ring) shown.

The 3D structures of these two inhibitors, respectively separated from complexes 2ITY [ 19 ] and 1M17 [ 62 ] in the PDB [ 54 ], are exhibited in Fig 2b and 2d respectively, and these structures were utilized as ligand templates in our major MD simulations.

Two WT EGFR kinase proteins (active form) in complexes 2ITY and 2ITZ [ 19 ] were regarded as our templates for the mutant prediction.

(e) Complex 2ITY (in PDB), composed of an active WT EGFR kinase (N-lobe + C-lobe) and an inhibitor (gefitinib); major gefitinib-interacting residues are labeled as red balls.

Publication Year: 2015


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