Citations in PubMed

Primary Citation PubMed: 12196540 Citations in PubMed

PDB ID Mentions in PubMed Central Article count: 32

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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BIM mediates EGFR tyrosine kinase inhibitor-induced apoptosis in lung cancers with oncogenic EGFR mutations.

(2007) PLoS Med 4

PubMed: 17973572 | PubMedCentral: PMC2043012 | DOI: 10.1371/journal.pmed.0040315

The Protein Data Bank ( http://www.pdb.org/ ) accession number for the EGFR tyrosine kinase domain with the 4-anilinoquinazoline inhibitor erlotinib is 1M17.

Publication Year: 2007


Alignment of protein structures in the presence of domain motions.

(2008) BMC Bioinformatics 9

PubMed: 18727838 | PubMedCentral: PMC2535786 | DOI: 10.1186/1471-2105-9-352

For the alignment between the structures of the protein kinase domains of CDK6 ( 1BI7 ), MAPK P38 ( 1P38 ), Src ( 1FMK ), IGF1 receptor ( 1JQH ), EGFR ( 1M17 ), HGFR ( 1R0P ) and JAK3 ( 1YVJ ), the al... orithm implemented in DALI can cope with many cases of different relative domain orientation.

Publication Year: 2008


Disruption of the EGFR E884-R958 ion pair conserved in the human kinome differentially alters signaling and inhibitor sensitivity.

(2009) Oncogene 28

PubMed: 19015641 | PubMedCentral: PMC2633425 | DOI: 10.1038/onc.2008.411

Structural Analysis EGFR crystal structures (PDB accession codes 1M17, 1XKK and 2GS6) ( Stamos et al. , 2002 ; Wood et al. , 2004 ; Zhang et al. , 2006 ) were analyzed using the program O ( Jones et a... . , 1991 ).

(B) EGFR kinase domain crystal structures [PDB accession codes 1M17 ( Stamos et al. , 2002 ) and 1XKK ( Wood et al. , 2004 )] when in complex with erlotinib (blue) and lapatinib (green) are shown.

Finally, we mapped the locations of the L858R and E884K mutations onto the three-dimensional structure of the EGFR kinase domain complexed with erlotinib and with lapatinib [PDB accession codes 1M17 ( Stamos et al. , 2002 ) and 1XKK ( Wood et al. , 2004 )] ( Figure 4B ).

The crystal structure of EGFR tyrosine kinase (PDB accession code: 1M17) ( Stamos et al. , 2002 ) was superimposed with the catalytic kinase domains of human CDK2 (PDB accession code: 1VYW) ( Pevarello et al. , 2004 ), human JNK3 (PDB accession code: 1PMQ) ( Scapin et al. , 2003 ), human insulin receptor kinase (PDB accession code: 1IR3) ( Hubbard, 1997 ), ZAP-70 tyrosine kinase (PDB accession code: 1U59) ( Jin et al. , 2004 ), LCK kinase (PDB accession code: 1QPD) ( Zhu et al. , 1999 ), and MET (PDB accession code: 2RFS) ( Bellon et al. , 2008 ) using Cα atoms in the program DeepView/Swiss-PdbViewer v3.7.

The crystal structure of EGFR tyrosine kinase (PDB accession code: 1M17) ( Stamos et al. , 2002 ) was superimposed with the catalytic kinase domains of human CDK2 (PDB accession code: 1VYW) ( Pevarello et al. , 2004 ), human JNK3 (PDB accession code: 1PMQ) ( Scapin et al. , 2003 ), human insulin receptor kinase (PDB accession code: 1IR3) ( Hubbard, 1997 ), ZAP-70 tyrosine kinase (PDB accession code: 1U59) ( Jin et al. , 2004 ), LCK kinase (PDB accession code: 1QPD) ( Zhu et al. , 1999 ) and MET (PDB accession code: 2RFS) ( Bellon et al. , 2008 ) using Cα atoms in the program DeepView/Swiss-PdbViewer v3.7.

Publication Year: 2009


Prediction of specificity-determining residues for small-molecule kinase inhibitors.

(2008) BMC Bioinformatics 9

PubMed: 19032760 | PubMedCentral: PMC2655090 | DOI: 10.1186/1471-2105-9-491

The 3D structure of CHK1 (PDB 2BRH , wire rendering with grey carbons) was superposed onto the structure of EGFR (hidden) in complex with OSI-774 (PDB 1M17 , ball and stick rendering with green carbon... ).

Table 1 S-Filter predictions Compound Primary target PDB Predictions FN FP TN TP Total SB-203580 p38 1A9U Leu 104 Thr 106 0 0 14 2 16 PHA-00781089 MK2 2P3G Cys 140 Gly 143 0 1 18 1 20 Roscovitine CDK2 2A4L Val 64 Leu 83 Ala 144 0 2 20 1 23 PP1 SRC/HCK 1QCF Thr 338 Gly 344 0 1 18 1 20 OSI-774 EGFR 1M17 Thr 766 Cys 773 0 1 19 1 21 GW-572016 EGFR 1XKK Cys 775 2 0 23 1 26 Fasudil ROCK1 2ESM Val 137 Met 153 Ala 215 1 2 14 1 17 Predicted specificity determinants are shown for each compound and are either designated as false positives (FP) or true positives (TP).

Publication Year: 2008


Optimal assignment methods for ligand-based virtual screening.

(2009) J Cheminform 1

PubMed: 20150995 | PubMedCentral: PMC2820492 | DOI: 10.1186/1758-2946-1-14

target number actives number decoys number clusters a PDB code b ace c 46 1796 19 p 1o86 ache d 100 3859 18 1eve cdk2 e 47 2070 32 1ckp cox2 f 212 12606 44 1cx2 egfr g 365 15560 40 1m17 fxa h 64 2092 ... 9 1f0r hivrt i 34 1494 17 1rt1 inha j 57 2707 23 1p44 p38 k 137 6779 20 1kv2 pde5 l 26 1698 22 1xp0 pdgfrb m 124 5603 22 1t46 src n 98 5679 21 2src vegfr2 o 48 2712 31 1fgi Overview of the used data sets containing the number of actives, decoys, different chemotype clusters, and the PDB code of the complexed crystal structure which contains the search query.

Publication Year: 2009


Application of 3D Zernike descriptors to shape-based ligand similarity searching.

(2009) J Cheminform 1

PubMed: 20150998 | PubMedCentral: PMC2820497 | DOI: 10.1186/1758-2946-1-19

Target PDB Actives Decoys Decoys per active angiotensin-converting enzyme (ace) 1o86 46 1796 39.04 acetylcholinesterase (ache) 1eve 100 3859 38.59 cyclin-dependent kinase 2(cdk2) 1ckp 47 2070 44.04 cy... looxygenase-2(cox2) 1cx2 212 12606 59.46 epidermal growth factor receptor(egfr) 1m17 365 15560 42.63 factor Xa(fxa) 1f0r 64 2092 32.69 HIV reverse transcriptase(hivrt) 1rt1 34 1494 43.94 enoyl ACP reductase(inha) 1p44 57 2707 47.49 P38 mitogen activated protein(p38) 1kv2 137 6779 49.48 phosphodiesterase(pde5) 1xp0 26 1698 65.31 platelet derived growth factor receptor kinase(pdgfrb) 1t46 124 5603 45.19 tyrosine kinase SRC(src) 2src 98 5679 57.95 vascular endothelial growth factor receptor(vegfr2) 1fgi 48 2712 56.5 The third dataset from the National Cancer Institute (NCI) consists of 42,687 compounds derived from an assay measuring protection from HIV-1 infection of human CEM cells [ 57 ].

Publication Year: 2009


Structure-based drug design and AutoDock study of potential protein tyrosine kinase inhibitors.

(2011) Bioinformation 5

PubMed: 21383902 | PubMedCentral: PMC3044423 | DOI: null

Docking evaluation for EGFRK inhibitors Compound IVc, 2-(1-piprazinylethyl)-6-fluoro-3, 4-dihydro-4-(3, 4- dihydroxy) phenoxy pyrido[3,4-d]pyrimidine, was bound into EGFRK (pdb code: 1m17) and exactly... superimposed on erlotinib (TarcevaTM) currently marketed for the treatment of non-small cell lung cancer.

Publication Year: 2011


In silico studies on marine actinomycetes as potential inhibitors for Glioblastoma multiforme.

(2011) Bioinformation 6

PubMed: 21584184 | PubMedCentral: PMC3089882 | DOI: null

Binding site analysis for the molecular targets against GBM The binding site for the two molecular targets including EphA2 and EGFR (PDB ID: 1MQB, 1M17) are known and were determined using PDBsum.

Methodology Protein preparation of the 3 molecular targets of GBM Docking studies were conducted on the three dimensional (3D) structures of the 3 molecular targets including EphA2, EGFR and EGFRvIII (PDB ID: 1MQB, 1M17 and 1I8I) which were obtained from protein data bank [ 36 ].

Docking using Glide extra precision All the ligands which were prepared using LigPrep were then subjected for docking against the 3 molecular targets including EphA2, EGFR and EGFRvIII (PDB ID: 1MQB, 1M17 and 1I8I) using Glide extra-precision (XP), version 5.5 [ 38 ] mode.

Before performing docking, hydrogen atoms and charges were added to these crystal structures of 1MQB, 1M17 and 1I8I and then the complex was submitted to a series of restrained, partial minimizations using the optimized potential for liquid simulations-all atom (OPLS-2005) force field [ 37 ].

Publication Year: 2011


Prediction of inhibitory activity of epidermal growth factor receptor inhibitors using grid search-projection pursuit regression method.

(2011) PLoS One 6

PubMed: 21811593 | PubMedCentral: PMC3141047 | DOI: 10.1371/journal.pone.0022367

g003 Figure 3 Crystal structure of EGFR bound to the 4-anilinoquinazoline inhibitor Erlotinib (PDB ID: 1M17).

Publication Year: 2011


VSDK: Virtual screening of small molecules using AutoDock Vina on Windows platform.

(2011) Bioinformation 6

PubMed: 21976864 | PubMedCentral: PMC3181425 | DOI: null

Another virtual screening was performed against EGFR tyrosine kinase (pdb code: 1m17) on a different computer whose specifications are: model; HP compaq, and cpu; AMD Sempron.

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


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


Erlotinib binds both inactive and active conformations of the EGFR tyrosine kinase domain.

(2012) Biochem J 448

PubMed: 23101586 | PubMedCentral: PMC3507260 | DOI: 10.1042/BJ20121513

Docking erlotinib on to wild-type EGFR-TKD in its active conformation, as described in the Experimental section, closely reproduced the binding mode observed crystallographically in PDB entry 1M17 [ 1... ] (see Supplementary Online Data and Supplementary Figure S4 at http://www.BiochemJ.org/bj/448/bj4480417add.htm ).

Parameter EGFR/erlotinib Data collection  Space group C 222 1  Cell dimensions    a , b , c (Å) 78.0, 114.3, 84.9   α, β, γ (°) 90, 90, 90  Resolution (Å) 50–2.75   R sym 0.159 (0.494)   I /σ 12.8 (2.1)  Completeness (%) 96.6 (82.1)  Redundancy 4.8 (2.8) Refinement  Resolution (Å) 50–2.75  Number of reflections 9413   R work / R free 0.23/0.25  Number of atoms   Protein 2201   Ligand 29   Water 34   B -factors   Protein 47.2   Ligand 47.5   Water 43.3  RMSDs   Bond lengths (Å) 0.009   Bond angles (°) 1.081 System preparation and molecular docking Active EGFR-TKD was modelled on the basis of PDB entries 1M17 (which also provided the initial erlotinib conformation) [ 10 ] and 2ITX [ 11 ], and the L834R mutant was modelled on the basis of PDB entry 2ITV [ 11 ].

( C ) Crystal structure from PDB entry 1M17 [ 10 ] showing erlotinib (magenta) bound to active EGFR-TKD.

Publication Year: 2012


Molecular modeling and description of a newly characterized activating mutation of the EGFR gene in non-small cell lung cancer.

(2012) Diagn Pathol 7

PubMed: 23088930 | PubMedCentral: PMC3523061 | DOI: 10.1186/1746-1596-7-146

Crystal structures of wildtype EGFR kinase domain without ligand (protein data bank entry 2gs2) and in complex with gefitinib (protein databank entry 1m17) served as templates for the homology modelin... calculations.

Publication Year: 2012


Virtual screening of specific insulin-like growth factor 1 receptor (IGF1R) inhibitors from the National Cancer Institute (NCI) molecular database.

(2012) Int J Mol Sci 13

PubMed: 23242155 | PubMedCentral: PMC3546745 | DOI: 10.3390/ijms131217185

The receptors and PDB IDs were CDK2 (1ckp), EGFr (1m17), FGFr1 (1agw), P38_MAP (1kv2), PDGFrb (model), SRC (2src), and VEGFr2 (1vr2).

Publication Year: 2012


2,2'-diphenyl-3,3'-diindolylmethane: a potent compound induces apoptosis in breast cancer cells by inhibiting EGFR pathway.

(2013) PLoS One 8

PubMed: 23555785 | PubMedCentral: PMC3610887 | DOI: 10.1371/journal.pone.0059798

Residues were numbered according to the PDB ID 1M17.

In silico EGFR Binding Study Structural information for the ATP binding domains of human EGFR (PDB ID: 1M17) was obtained from Protein Data Bank.

PDB IDs 1M17 and 3UG2 were used.

Publication Year: 2013


Optimization of substituted 6-salicyl-4-anilinoquinazoline derivatives as dual EGFR/HER2 tyrosine kinase inhibitors.

(2013) PLoS One 8

PubMed: 23936329 | PubMedCentral: PMC3731256 | DOI: 10.1371/journal.pone.0069427

These results were mainly derived from two molecular docking studies, in which one was performed between compounds 9–27 , Erlotinib and the EGFR protein (PDB code: 1M17), while the other one w... s performed between compounds 5–25 , TAK-285 and the HER2 protein (PDB code: 3RCD).

g003 Figure 3 Docking model of the initial compound 1 and compound 21 bound to the active sites of the EGFR and HER2 proteins (PDB code: 1M17 and 3RCD, respectively).

Molecular docking Docking study was performed to fit compound 21 into the active center of the two protein-ligand complexes of the epidermal growth factor family (PDB code: 1M17 and 3RCD, respectively).

Two groups of molecular dockings between these novel 4-anilinoquinazoline analogs and two protein-ligand complexes (as for EGFR, PDB code: 1M17; as for HER2, PDB code: 3RCD) retrieved from the RCSB Protein Data Bank were performed, and the obtained results were plotted as a line-scatter graph and presented in Figure 5 , describing the CDOCKER_INTERACTION_ENERGY of two sets of molecular dockings.

Molecular docking studies based on EGFR and HER2 co-crystal structures (EGFR pdb code: 1M17, and HER2 pdb code: 3RCD) suggested that compound 1 would fit into the ATP-binding site of the HER2/EGFR protein ( Figure 3A, 3B, 3D, and 3E ).

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


PubMed ID is not available.

Published in 2010

PubMedCentral: PMC3823453

The 30 amino acid sequence from the epidermalgrowth factor receptor (EGFR; PBD code: 1m17) and the correspondingstructure served as template for the modellingof the N-terminalparts of the Jak pseudoki... ase domains (e.g. exon 12 region inJak2).

Publication Year: 2010


Network understanding of herb medicine via rapid identification of ingredient-target interactions.

(2014) Sci Rep 4

PubMed: 24429698 | PubMedCentral: PMC3893644 | DOI: 10.1038/srep03719

Previous study on erlotinib-EGFR interaction showed that the N1 of the erlotinib quinazoline accepts an hydrogen from the Met769 amide nitrogen, and the other quinazoline nitrogen atom (N3) bridges th... hydrogen bond with Thr766 side chain via a water molecule (PDB ID: 1M17) 27 .

Publication Year: 2014


Implementation of the Hungarian algorithm to account for ligand symmetry and similarity in structure-based design.

(2014) J Chem Inf Model 54

PubMed: 24410429 | PubMedCentral: PMC3958141 | DOI: 10.1021/ci400534h

Scoring Function To illustrate the first extended application, we examined docked results from an enrichment study previously performed in our laboratory, in which Balius et al. 40 docked 475 known ac... ive and 15 990 decoy compounds to the target epidermal growth factor receptor (EGFR, PDB 1M17).

Publication Year: 2014


PubMed ID is not available.

Published in 2014

PubMedCentral: PMC4049246

Figure 1 Crystal structures of the EGFR ATP-binding pocket with (A) erlotinib (PDB ID: 1M17) 15 and (B) lapatinib (PDB ID: 1XKK) 9 reveal the inhibitor binding modes.

Crystal structures of the kinase domain of EGFR with either erlotinib (1M17) 15 or lapatinib (1XKK) 9 (Figure 1 A,B) show that while the pharmacophore arm is oriented deep in the binding pocket, the 6-position is amenable to chemical modification without perturbing the key conserved contacts of the binding pocket.

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


QSAR-based models for designing quinazoline/imidazothiazoles/pyrazolopyrimidines based inhibitors against wild and mutant EGFR.

(2014) PLoS One 9

PubMed: 24992720 | PubMedCentral: PMC4081576 | DOI: 10.1371/journal.pone.0101079

Receptor-ligand Preparation for docking Protein (EGFR kinase, PDB ID: 1M17 and L858R mutant EGFR, PDB ID: 2ITZ) [15] , [29] and ligand (EGFR inhibitor, Erlotinib and IRESSA) preparation was performed ... sing the AutoDock 4.2 tool [30] , which involved the addition of hydrogen atoms, computing charges, merging non-polar hydrogen atoms and defining AD4 atom types to ensure that atom conformed to the AutoDock atom types.

Therefore, we carried out molecular docking for the 128 experimentally known EGFR inhibitors at the active binding site of PDB: 1M17 [29] .

Our docked structure is overlaid on the top of Erlotinib bound EGFR cristal stucture (PDB ID: 1M17).

Publication Year: 2014


PubMed ID is not available.

Published in 2014

PubMedCentral: PMC4114474

The DUD proteins include acetycholinesterase AChE (PDB code: 1EVE), human androgen receptor AR (PDB code: 1XQ2), human cyclin-dependent kinase 2 CDK2 (PDB code: 1CKP), human epidermal growth factor re... eptor EGFR (PDB code: 1M17), human mitogen-activated protein kinase 14 known as p38 (PDB code: 1KV2), human proto-oncogene tyrosine-protein kinase Src (PDB code: 2SRC), and cationic trypsin (PDB code: 1BJU).

Publication Year: 2014


Protein redox chemistry: post-translational cysteine modifications that regulate signal transduction and drug pharmacology.

(2014) Front Pharmacol 5

PubMed: 25339904 | PubMedCentral: PMC4186267 | DOI: 10.3389/fphar.2014.00224

(D) Binding of small molecule inhibitors to the WT EGFR active site is shown in context of Cys 797 (yellow; PDB 1M17).

Publication Year: 2014


Epidermal growth factor receptor (EGFR) mutations in lung cancer: preclinical and clinical data.

(2014) Braz J Med Biol Res 47

PubMed: 25296354 | PubMedCentral: PMC4230282 | DOI: null

A , Structure of the kinase domain of EGFR in complex with erlotinib (based on Protein Data Bank [PDB] accession code 1M17) and location of the most common EGFR mutations.

Publication Year: 2014


PubMed ID is not available.

Published in 2015

PubMedCentral: PMC4368709

The structure visualization was based on Protein Data Bank structure models 1nql, 1ivo, 2jwa, 1m17 and 2gs6[ 47 – 50 ].

Publication Year: 2015


PubMed ID is not available.

Published in 2015

PubMedCentral: PMC4414309

( A ) AL776 modeled in the EGFR kinase-binding pocket using the Protein Data Bank (PDB) with code 1M17.

AL776 was modeled in the EGFR kinase pocket using the 1M17 Protein Data Bank (PDB) structure as a starting point.

Molecular Modeling AL776 was modeled in the EGFR kinase pocket using the Protein Data Bank (PDB) structure [ 26 ] with code 1M17 downloaded from www.rcsb.org .

Despite the large size of AL776, the quinazoline moiety could bind to the 1M17 structure in a pose analogous to erlotinib.

Publication Year: 2015


PubMed ID is not available.

Published in 2015

PubMedCentral: PMC4439022

(c) and (d), The structures of erlotinib (PDB: 1M17), 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.

Publication Year: 2015


PubMed ID is not available.

Published in 2015

PubMedCentral: PMC4468516

The kinase-drug complex structures and the mutant EGFR structure (PDB 3W2P) are superimposed on the structure of wild-type EGFR, including EGFR-gefitinib (PDB 2IVT) and EGFR-erlotinib (PDB 1M17) compl... x structures.

Publication Year: 2015


PubMed ID is not available.

Published in 2015

PubMedCentral: PMC4517520

Based on the sequence of wild-type EGFR protein (PDB code: 1M17), the other 41 EGFR protein sequences were aligned together by Discovery Studio 3.5 ( Figure 3A ).

In order to investigate the binding pockets of EGFR proteins, all the 42 EGFR protein–ligand complexes were superposed together based on the 1M17 protein template ( Figure 3A ).

( C ) Mapping the ligands (Erlotinib in 1M17 EGFR protein and lapatinib in 1XKK EGFR protein) into subregions of the binding pockets in the 3D view.

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 position (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