PMID-sentid Pub_year Sent_text comp_official_name comp_offsetprotein_name organism prot_offset 33096664-10 2020 However, molecular dynamics simulations demonstrated that only ZINC16525481 and ZINC38484632 which have good binding free energy and stable hydrogen bonding interactions with EGFR and VEGFR2. Hydrogen 140-148 epidermal growth factor receptor Homo sapiens 175-179 33374155-5 2020 Our synthesized compounds were promising, demonstrating high selectivity and affinity for EGFR/HER2, especially the hinge region forming a hydrophobic pocket, which was mediated by hydrogen bonding as well as hydrophobic and electrostatic interactions, as indicated by molecular modeling. Hydrogen 181-189 epidermal growth factor receptor Homo sapiens 90-94 32653374-6 2020 The thermodynamic analysis showed that van der Waals and hydrogen binding forces play a major role in the interaction of erlotinib with EGFR. Hydrogen 57-65 epidermal growth factor receptor Homo sapiens 136-140 32440336-7 2020 The molecular docking studies suggest hydrogen bonding, hydrophobic and pi-pair interactions with the active site of epidermal growth factor receptor, vascular endothelial growth factor receptor 2 and lipoxygenase receptors. Hydrogen 38-46 epidermal growth factor receptor Homo sapiens 117-149 32139324-4 2020 Compounds 1e and 1h were identified as lead compounds which displayed almost 3-4 times more potent inhibition of EGFR and HER2 than the approved drug lapatinib. Hydrogen 17-19 epidermal growth factor receptor Homo sapiens 113-117 31710991-5 2019 Based on the predicted activity and XP glide score, three EGFR inhibitors were synthesized and characterized using 1H-NMR, 13C-NMR and MS. Hydrogen 115-117 epidermal growth factor receptor Homo sapiens 58-62 31787359-9 2020 The introduction of extra hydrogen bond interaction with mutant Ser797 is efficient method for the design of the fourth-generation EGFR-TKIs. Hydrogen 26-34 epidermal growth factor receptor Homo sapiens 131-135 30652647-10 2020 Molecular docking studies on EGFR (PDB ID: 1M17) results, the compounds 6d, 6j and 6l showed good dock/PLP scores i.e.-81.28, -73.98 and -75.37 by interacting with Leu-694, Val-702and Gly-772 amino acids via hydrophobic and hydrogen bonds with Asn818 and Met-769. Hydrogen 224-232 epidermal growth factor receptor Homo sapiens 29-33 31241919-11 2019 In silico studies indicated hydrogen bonding, hydrophobic, and pi-pair (pi-pi, pi-sigma, and pi-cation) interactions between the complexes and EGFR/VEGFR2 kinase receptors. Hydrogen 28-36 epidermal growth factor receptor Homo sapiens 143-147 31536605-9 2019 Additionally, the interaction between EGFR and ATP was favored by DeltaELREA EGFR over wild-type EGFR, as reflected by the number of hydrogen bonds formed and the free energy of binding. Hydrogen 133-141 epidermal growth factor receptor Homo sapiens 38-42 31536605-9 2019 Additionally, the interaction between EGFR and ATP was favored by DeltaELREA EGFR over wild-type EGFR, as reflected by the number of hydrogen bonds formed and the free energy of binding. Hydrogen 133-141 epidermal growth factor receptor Homo sapiens 77-81 31536605-9 2019 Additionally, the interaction between EGFR and ATP was favored by DeltaELREA EGFR over wild-type EGFR, as reflected by the number of hydrogen bonds formed and the free energy of binding. Hydrogen 133-141 epidermal growth factor receptor Homo sapiens 77-81 30716685-4 2019 We found that the hydrogen bond network of proteins (three states of EGFR) was affected by Tubemoside. Hydrogen 18-26 epidermal growth factor receptor Homo sapiens 69-73 30593826-0 2019 Hydrogen bond analysis of the EGFR-ErbB3 heterodimer related to non-small cell lung cancer and drug resistance. Hydrogen 0-8 epidermal growth factor receptor Homo sapiens 30-34 30607149-4 2018 Based on the results, the compounds L1, L2, L4, L5, L6, L7, L10, L15, and L18 may be promising EGFR inhibitors based on docking score and hydrogen bonds. Hydrogen 138-146 epidermal growth factor receptor Homo sapiens 95-99 31223050-7 2019 The hydrogen bonds, hydrophobic interactions, atomic pi-cation interactions and salt bridges of ligands are contributing additional stability to receptor structure, which can lead to blocking the intracellular protein-tyrosine kinase activity, including EGFR associated pathways activation in NSCLC. Hydrogen 4-12 epidermal growth factor receptor Homo sapiens 254-258 30607149-8 2018 The results indicated that the three compounds bound to EGFR active site in a stable manner during the simulation through the formation of new hydrogen bonds with Phe699, Leu694, Gly700, Lys721, Met769, Arg817, and Asp831 with the superiority of compound L15. Hydrogen 143-151 epidermal growth factor receptor Homo sapiens 56-60 29421573-4 2018 Molecular docking showed that 8d can form four hydrogen bonds with EGFR, and two of them were located in the Asp855-Phe856-Gly857 (DFG) motif of EGFR. Hydrogen 47-55 epidermal growth factor receptor Homo sapiens 67-71 29571113-8 2018 In molecular docking studies compound 5a was bound to the active pocket of the EGFR (PDB 1M17) with five key hydrogen bonds and two pi-pi interaction with binding energies DeltaG = -34.581 Kcal/mol. Hydrogen 109-117 epidermal growth factor receptor Homo sapiens 79-83 29363191-6 2018 Furthermore, thermodynamic analysis indicated that the hydrogen bond or Van der Waals force was the main interaction force in the process of EGFR binding to all 5 ligands. Hydrogen 55-63 epidermal growth factor receptor Homo sapiens 141-145 29466773-8 2018 The predicted hydrogen bond interaction formed by a small molecule inhibitor with mutant Ser797 is available to design the fourth-generation EGFR-TKIs. Hydrogen 14-22 epidermal growth factor receptor Homo sapiens 141-145 29207336-6 2018 Docking simulation studies against the two proteins EGFR and DHFR demonstrate that compound 8 showed higher binding affinity toward the two proteins more than compound 5, suggesting that trimethoxy groups may be responsible for this higher activity through the formation of five hydrogen bonding with the active domain (4r3r) and other four interactions with the active domain (1dls). Hydrogen 279-287 epidermal growth factor receptor Homo sapiens 52-56 29462206-8 2018 Examination of the crystal structure of cell-free synthesized 059-152-Fv in complex with the extracellular domain of human EGFR revealed that the epitope of 059-152-Fv broadly covers the EGF binding surface on domain III, including residues that formed critical hydrogen bonds with EGF (Asp355EGFR, Gln384EGFR, H409EGFR, and Lys465EGFR), so that the antibody inhibited EGFR activation. Hydrogen 262-270 epidermal growth factor receptor Homo sapiens 123-127 27691399-9 2017 Suitable position and orientation of GLU in residue 100 of 7D12 against related amino acids of EGFR formed some extra hydrogen and electrostatic interactions which resulted in binding enhancement. Hydrogen 118-126 epidermal growth factor receptor Homo sapiens 95-99 28482570-6 2017 The molecular docking studies of the heteroleptic silver(I) complexes with EGFR/VEGFR2 kinase receptors show hydrophobic, pi-pi, sigma-pi and hydrogen bonding interactions. Hydrogen 142-150 epidermal growth factor receptor Homo sapiens 75-79 28290719-3 2017 Similarly, the pharmacophore model for EGFR (T790M) (r2 = 0.92, q2 = 0.72) suggested that the presence of a hydrogen bond acceptor, two hydrogen bond donors and a hydrophobic group plays vital role in binding of an inhibitor of EGFR (T790M). Hydrogen 108-116 epidermal growth factor receptor Homo sapiens 39-43 28290719-3 2017 Similarly, the pharmacophore model for EGFR (T790M) (r2 = 0.92, q2 = 0.72) suggested that the presence of a hydrogen bond acceptor, two hydrogen bond donors and a hydrophobic group plays vital role in binding of an inhibitor of EGFR (T790M). Hydrogen 108-116 epidermal growth factor receptor Homo sapiens 228-232 28290719-3 2017 Similarly, the pharmacophore model for EGFR (T790M) (r2 = 0.92, q2 = 0.72) suggested that the presence of a hydrogen bond acceptor, two hydrogen bond donors and a hydrophobic group plays vital role in binding of an inhibitor of EGFR (T790M). Hydrogen 136-144 epidermal growth factor receptor Homo sapiens 39-43 26763193-3 2016 A simulated six-membered ring strategy formed through intramolecular hydrogen bonds was employed to mimic the planar quinazoline of the EGFR antagonist, gefitinib. Hydrogen 69-77 epidermal growth factor receptor Homo sapiens 136-140 27524310-7 2016 Compounds 1c-1f, 1h effectively inhibited the in vitro kinase activity of EGFR and HER2 with similar efficacy as gefitinib and erlotinib. Hydrogen 17-19 epidermal growth factor receptor Homo sapiens 74-78 24954438-5 2015 In the molecular modeling study, compound 12b was bound into the active pocket of EGFR with two hydrogen bond and with minimum binding free energy Gb = -25.1125 kcal/mol. Hydrogen 96-104 epidermal growth factor receptor Homo sapiens 82-86 26096169-5 2016 It was found that the insertion and duplication mutations in exon 20 can generally cause drug resistance to EGFR due to the reduced size of kinase"s active pocket, while deletion mutations in exon 19 associate closely with increased inhibitor sensitivity to EGFR by establishing additional non-bonded interactions across complex interface, including hydrogen bonds, cation-pi interactions and hydrophobic contacts. Hydrogen 350-358 epidermal growth factor receptor Homo sapiens 108-112 26096169-5 2016 It was found that the insertion and duplication mutations in exon 20 can generally cause drug resistance to EGFR due to the reduced size of kinase"s active pocket, while deletion mutations in exon 19 associate closely with increased inhibitor sensitivity to EGFR by establishing additional non-bonded interactions across complex interface, including hydrogen bonds, cation-pi interactions and hydrophobic contacts. Hydrogen 350-358 epidermal growth factor receptor Homo sapiens 258-262 26629323-11 2015 A docking simulation between JAK3 inhibitor VI and the ATP-binding pocket of EGFR T790M/L858R predicted a potential binding status with hydrogen bonds. Hydrogen 136-144 epidermal growth factor receptor Homo sapiens 77-81 25175686-4 2015 We have designed and synthesized a series of 6-methoxy-7-(3-morpholinopropoxy)-1-(2- phenoxyethyl)-quinoxalin-2(1H)-one derivatives as novel EGFR inhibitors. Hydrogen 112-114 epidermal growth factor receptor Homo sapiens 141-145 25305687-1 2014 The interactions of gefitinib (Iressa) in EGFR are hydrogen bonding and van der Waals forces through quinazoline and aniline rings. Hydrogen 51-59 epidermal growth factor receptor Homo sapiens 42-46 25172421-6 2014 In the molecular modelling study, compound 9i was bound in to the active pocket of EGFR with four hydrogen bonds and two pi-cation interactions having minimum binding energy DeltaGb=-54.4 kcal/mol. Hydrogen 98-106 epidermal growth factor receptor Homo sapiens 83-87 24607998-6 2014 In the molecular modeling study, compound 7k was bound in to the active pocket of EGFR with three hydrogen bond and one pi-cation interaction with minimum binding energy DeltaGb = -54.6913 kcal/mol, as well as compound 7b was bound in to the active site of FabH with hydrogen bond and pi-sigma interactions with minimum binding energy DeltaGb = -45.9125 kcal/mol. Hydrogen 98-106 epidermal growth factor receptor Homo sapiens 82-86 24853453-4 2014 18alpha-GAMG was firstly nicely bound to epidermal growth factor receptor (EGFR) via six hydrogen bonds and one charge interaction, and the docking calculation proved the correlation between anticancer activities and EGFR inhibitory activities. Hydrogen 89-97 epidermal growth factor receptor Homo sapiens 41-73 24853453-4 2014 18alpha-GAMG was firstly nicely bound to epidermal growth factor receptor (EGFR) via six hydrogen bonds and one charge interaction, and the docking calculation proved the correlation between anticancer activities and EGFR inhibitory activities. Hydrogen 89-97 epidermal growth factor receptor Homo sapiens 75-79 24607998-6 2014 In the molecular modeling study, compound 7k was bound in to the active pocket of EGFR with three hydrogen bond and one pi-cation interaction with minimum binding energy DeltaGb = -54.6913 kcal/mol, as well as compound 7b was bound in to the active site of FabH with hydrogen bond and pi-sigma interactions with minimum binding energy DeltaGb = -45.9125 kcal/mol. Hydrogen 267-275 epidermal growth factor receptor Homo sapiens 82-86 24411123-7 2014 Compounds 1b-1f, 1h effectively inhibited the in vitro kinase activity of EGFR and HER2 with similar efficacy as erlotinib and gefitinib. Hydrogen 17-19 epidermal growth factor receptor Homo sapiens 74-78 23538097-7 2013 SF-induced phosphorylation of EGFR for 1h was partly reversible upon removal of the dendrimer and examination of cells 24 later. Hydrogen 39-41 epidermal growth factor receptor Homo sapiens 30-34 24269511-4 2014 SAR and docking studies allowed the identification of pharmacophoric groups for both kinases and demonstrated the importance of a hydrogen bond donor at the para position of the aniline moiety for interaction with conserved Glu and Asp amino acids in EGFR and VEGFR-2 binding sites. Hydrogen 130-138 epidermal growth factor receptor Homo sapiens 251-255 21426301-4 2011 We find that in the active conformation of the ErbB kinases, key subdomain motions are co-ordinated through conserved hydrophilic interactions: activating bond-networks consisting of hydrogen bonds and salt bridges. Hydrogen 183-191 epidermal growth factor receptor Homo sapiens 47-51 23490150-4 2013 An X-ray co-crystal structure of 19b with EGFR demonstrated that the N-1 and N-3 nitrogens of the pyrimido[4,5-b]azepine scaffold make hydrogen-bonding interactions with the main chain NH of Met793 and the side chain of Thr854 via a water-mediated hydrogen bond network, respectively. Hydrogen 135-143 epidermal growth factor receptor Homo sapiens 42-46 22486613-6 2012 The inhibitor exhibits extensive interactions with the EGFR catalytic site in the form of hydrogen bonds, pi-pi bond and salt bridges. Hydrogen 90-98 epidermal growth factor receptor Homo sapiens 55-59 22414612-7 2012 The binding mode of 1 from docking simulation in the EGFR active site revealed that the urea motif formed hydrogen bonding with Lys745, Thr854 and Asp855 in hydrophobic pocket of EGFR. Hydrogen 106-114 epidermal growth factor receptor Homo sapiens 53-57 22414612-7 2012 The binding mode of 1 from docking simulation in the EGFR active site revealed that the urea motif formed hydrogen bonding with Lys745, Thr854 and Asp855 in hydrophobic pocket of EGFR. Hydrogen 106-114 epidermal growth factor receptor Homo sapiens 179-183 20877636-3 2010 We previously outlined the mode of binding between the TKB domain and various substrate peptide motifs, including epidermal growth factor receptor (EGFR) and Sprouty2 (Spry2), and demonstrated that an intrapetidyl hydrogen bond forms between the (pY-1) arginine or (pY-2) asparagine and the phosphorylated tyrosine, which is crucial for binding. Hydrogen 214-222 epidermal growth factor receptor Homo sapiens 114-146 25346782-8 2011 In HER2, we also predict a role for phosphorylated Y877 in bridging a network of hydrogen bonds that fasten the A-loop in its active conformation, suggesting that HER2 may be unique among the ErbB members in requiring A-loop tyrosine phosphorylation for functionality. Hydrogen 81-89 epidermal growth factor receptor Homo sapiens 192-196 20877636-3 2010 We previously outlined the mode of binding between the TKB domain and various substrate peptide motifs, including epidermal growth factor receptor (EGFR) and Sprouty2 (Spry2), and demonstrated that an intrapetidyl hydrogen bond forms between the (pY-1) arginine or (pY-2) asparagine and the phosphorylated tyrosine, which is crucial for binding. Hydrogen 214-222 epidermal growth factor receptor Homo sapiens 148-152 20471394-7 2010 The capability for multiple polar interactions, along with hydrogen bonding between TM segments, correlates with the observed highest affinity of the ErbB1/ErbB2 heterodimer, implying an important contribution of the TM helix-helix interaction to signal transduction. Hydrogen 59-67 epidermal growth factor receptor Homo sapiens 150-155 19559571-7 2009 RESULTS: HB-EGF-induced phosphorylation of EGFR with maximum phosphorylation at 1h. Hydrogen 80-82 epidermal growth factor receptor Homo sapiens 43-47 15177440-3 2004 To perceive the exact mode of binding of these ligands, two models of the ligand-EGFR complexes were considered: (1) reversible binding mode in which the ligand had hydrogen bond interactions at the binding site and (2) irreversible binding mode wherein the ligand"s Michael acceptor side chain has proximity to the sulfhydryl group of C773 of EGFR, thereby enabling a covalent interaction. Hydrogen 165-173 epidermal growth factor receptor Homo sapiens 81-85 18199660-0 2008 The kinetics of the hydrogen/deuterium exchange of epidermal growth factor receptor ligands. Hydrogen 20-28 epidermal growth factor receptor Homo sapiens 51-83 18199660-1 2008 Five highly homologous epidermal growth factor receptor ligands were studied by mass spectral analysis, hydrogen/deuterium (H/D) exchange via attenuated total reflectance Fourier transform-infrared spectroscopy, and two-dimensional correlation analysis. Hydrogen 104-112 epidermal growth factor receptor Homo sapiens 23-55 18053681-7 2008 The expression of EGFR and ErbB2 receptors was significantly reduced after 1h and 4h of treatment while ErbB2 receptor was significantly increased and EGFR receptor returned to basal value after 24h. Hydrogen 75-77 epidermal growth factor receptor Homo sapiens 18-22 16275081-2 2006 A strategy of pseudo six-membered ring formed through intramolecular hydrogen bonding in salicylanilides is employed to mimic the planar pyrimidine ring of quinazoline EGFR inhibitors. Hydrogen 69-77 epidermal growth factor receptor Homo sapiens 168-172 15993078-4 2005 Compounds having 5-anilino substituent exhibit high potency with 5-(4-methoxy)anilino-4-hydroxy-8-nitroquinazoline (1h) being the best dual EGFR/ErbB-2 inhibitors, which effectively inhibited the growth of both EGFR (MDA-MB-468, IC(50)<0.01microM) and ErbB-2 (SK-BR-3, IC(50)=13microM) overexpressing human tumor cell lines in vitro. Hydrogen 116-118 epidermal growth factor receptor Homo sapiens 140-144 15993078-4 2005 Compounds having 5-anilino substituent exhibit high potency with 5-(4-methoxy)anilino-4-hydroxy-8-nitroquinazoline (1h) being the best dual EGFR/ErbB-2 inhibitors, which effectively inhibited the growth of both EGFR (MDA-MB-468, IC(50)<0.01microM) and ErbB-2 (SK-BR-3, IC(50)=13microM) overexpressing human tumor cell lines in vitro. Hydrogen 116-118 epidermal growth factor receptor Homo sapiens 211-215 15571862-6 2004 An X-ray analysis of 10a including water and DMF illustrates a possible hydrogen bond pattern and could serve as information for preferred receptor (e.g. EGFR tyrosine kinase) binding sites. Hydrogen 72-80 epidermal growth factor receptor Homo sapiens 154-158 11755203-8 2001 Hydrogen bonds and hydrophobic interaction appear to be important in the binding of these inhibitors to EGFR. Hydrogen 0-8 epidermal growth factor receptor Homo sapiens 104-108 14561085-9 2003 They are more likely to have multiple binding modes at the ATP site of EGFR, i.e., either modes A or B, than in the ATP site of HER-2 where they are possibly limited to only binding mode, A. Selectivity of the methoxy compounds on the other hand appears to depend on hydrogen bonding interactions involving the cyano group and residue 751 in the ATP site. Hydrogen 267-275 epidermal growth factor receptor Homo sapiens 71-75 34271119-8 2021 Both hydrophobic interactions and hydrogen bonds contributed to the 20(R, S)-PPT-EGFR binding. Hydrogen 34-42 epidermal growth factor receptor Homo sapiens 81-85 34633106-11 2022 A docking model shows that NP1 interacted primarily with TK-EGFR via hydrogen bonding. Hydrogen 69-77 epidermal growth factor receptor Homo sapiens 57-64 35578853-8 2022 RESULTS: In the tested example, SEPA bash script was able to identify the tripeptide YYH ranked within top 20 based on the essential hydrogen bond interaction towards the essential amino acid residue ASP837 in the EGFR-TK receptor. Hydrogen 133-141 epidermal growth factor receptor Homo sapiens 214-218 34097593-8 2022 Molecular docking model displayed a hydrogen bond between Met-769 amide nitrogen and N-1 in pteridine motif of 7m which lay at the ATP binding site of EGFR kinase domain. Hydrogen 36-44 epidermal growth factor receptor Homo sapiens 151-155 35129191-4 2022 We demonstrated that TANVBC71 was absorbed faster in high amounts by cancer cells than nanovesicles owing to its high affinity for the epidermal growth factor receptor and extracellular matrix components that are driven by van der Waals attraction as well as hydrogen bonding and hydrophobic interactions in a complex manner. Hydrogen 259-267 epidermal growth factor receptor Homo sapiens 135-167 35381900-9 2022 The data obtained from hydrogen bond analysis revealed a more equilibrated and stable form of the ClyA-affiEGFR-GALA structure upon interaction with EGFR. Hydrogen 23-31 epidermal growth factor receptor Homo sapiens 149-153 35178955-11 2022 Molecular docking showed that PPI bound to the extracellular domain of EGFR and formed hydrogen bond with Gln366 residue. Hydrogen 87-95 epidermal growth factor receptor Homo sapiens 71-75 33858315-12 2022 Molecular docking reveals involvement of one hydrogen bond with Met793 in binding with EGFR however; it was not stable during simulation and these compounds bind to the receptor mainly via hydrophobic contacts. Hydrogen 45-53 epidermal growth factor receptor Homo sapiens 87-91 32698735-9 2021 Molecular docking studies proved that the compound R8 has good binding fitting by forming hydrogen bonds with amino acid residues at ATP binding sites of EGFR. Hydrogen 90-98 epidermal growth factor receptor Homo sapiens 154-158 32698735-12 2021 Molecular docking studies reveled that compound R8 has good fitting by forming different Hydrogen bonding interactions with amino acids at ATP binding site of epidermal growth factor receptor target. Hydrogen 89-97 epidermal growth factor receptor Homo sapiens 159-191 33161110-7 2021 Molecular docking suggested that the CuIIb-EGFR binding fundamentally depends on the contribution of both hydrophobic and hydrogen-bonding interactions. Hydrogen 122-130 epidermal growth factor receptor Homo sapiens 43-47