Citations in PubMed

Primary Citation PubMed: 16777603 Citations in PubMed

PDB ID Mentions in PubMed Central Article count: 11

Citations in PubMed

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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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ATP and MO25alpha regulate the conformational state of the STRADalpha pseudokinase and activation of the LKB1 tumour suppressor.

(2009) PLoS Biol 7

PubMed: 19513107 | PubMedCentral: PMC2686265 | DOI: 10.1371/journal.pbio.1000126

Residues from the C-lobe of STRADα (152–431) were superimposed onto the structures of inactive CDK2 (PDB ID 1HCK [56] ) and EGFR kinase (PDB ID 2GS7), and active CDK2 (... DB ID 1JST) and EGFR (PDB ID 2GS2).

Publication Year: 2009

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

The initial ABL and EGFR structures that converged during homology modeling refinement to the crystallographic active conformations of the mutants correspond to the Src-like inactive ABL (pdb entry 2G... T) and Src-like inactive EGFR (pdb entry 2GS7).

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 structure), 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).

(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).

For simulations with the EGFR dimers, we utilized the crystal structure of the EGFR in the inactive state (pdb entry 2GS7).

Similarly, MD simulations of the EGFR kinase domain were initiated for EGFR-WT, EGFR-T790M, EGFR-L858R from the Src/Cdk-like inactive structures (pdb entries 1XKK, 2GS7), and active conformational form (pdb entry 2G6M).

Upper Panel: Color-coded mapping of the averaged protein flexibility profiles (RMSF values) from MD simulations of the symmetric EGFR dimer (pdb entry 2GS7).

MD simulations of EGFR-WT (in blue), and EGFR-T790M (in red) were performed using the inactive EGFR dimer (pdb entry 2GS7).

Publication Year: 2009

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

The depicted mapping and analysis of allosteric communications is based on simulations of the crystal structure of an asymmetric EGFR dimer (PDB ID 2GS6) and inactive symmetric dimer (PDB ID 2GS7).

Based on this crystal structure of a symmetric EGFR dimer (PDB ID 2GS7 [117] ), it was initially proposed that the “electrostatic hook” formed between the C-terminal tail (residues 979–990) and the hinge region in the kinase domain may stabilize structural topology of a symmetric dimer ( Figures 9 A, B ).

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] .

( A ) An overview of the inter-monomer interface in the crystal structure of a symmetric inactive EGFR dimer (PDB ID 2GS7).

Publication Year: 2011

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

Inactive EGFR-TKD was modelled based on PDB entries 2GS7 [ 12 ] and 1XKK [ 13 ].

Publication Year: 2012

Ab initio modeling and experimental assessment of Janus Kinase 2 (JAK2) kinase-pseudokinase complex structure.

(2013) PLoS Comput Biol 9

PubMed: 23592968 | PubMedCentral: PMC3616975 | DOI: 10.1371/journal.pcbi.1003022

(A) The sequence alignment of αC helix and activation loop of JAK2 kinase domain with EGFR (PDB id: 2GS7) was used to build the inactive conformation of the JH1 kinase domain.

We next modeled JH1 in the inactive conformation based on the inactive conformation of EGFR (PDB ID: 2GS7) and examined the pattern of correlated motions using MutInf ( Figures 4A–B , and S2A–B).

We modeled the JAK2 kinase domain in the inactive conformation (residues 840–1132) using its active conformation structure as a template (PDB id: 2B7A) [37] , with the αC helix (residues 882–928) and activation loop (residues 992–1018) modeled from the inactive conformation of EGFR (PDB id: 2GS7) [15] .

Publication Year: 2013

Utilizing protein structure to identify non-random somatic mutations.

(2013) BMC Bioinformatics 14

PubMed: 23758891 | PubMedCentral: PMC3691676 | DOI: 10.1186/1471-2105-14-190

in cluster P-Value 1 751 858 4 1.35E-04 2 719 751 2 2.41E-03 3 790 858 2 2.82E-03 Figure 5 The EGFR Structure (PDB ID 2GS7)(structure color coded by region: 1) (cluster 1 - light blue and yellow, 2) (... luster 2 - blue and 3) cluster 3 - yellow.

Publication Year: 2013

Coarse-grained molecular simulation of epidermal growth factor receptor protein tyrosine kinase multi-site self-phosphorylation.

(2014) PLoS Comput Biol 10

PubMed: 24453959 | PubMedCentral: PMC3894164 | DOI: 10.1371/journal.pcbi.1003435

This structure was built up largely from the known structure of the EGFR extracellular domain with bound EGF in a 2∶2 “dimeric” complex (3NJP) [17] and an asymmetric PTK domain... dimer structure formed from individual active (2GS6) and inactive (2GS7) conformation kinase structures [4] (see Materials and Methods ).

Thus, in this work, the apposition of active (receiver) and inactive (activator) conformation PTK domains in an asymmetric dimer structure was effected by superpositioning an inactive conformation kinase structure (2GS7, residues 679 to 959) upon the activator-orientated kinase (residue 669 to 967) in a kinase dimer generated from the active-conformation crystal structure 2GS6 by a symmetry operation.

Then, as residues 655 to 664 of the JM sequence are believed to assume an α-helical conformation in both activator and receiver kinases [3] but are not included in the inactive conformation kinase structure (2GS7) used for the activator in our symmetric dimer model, we positioned a copy of this short helical structure from 3GOP near the activator kinase N-terminus, such that it might be joined to the activator kinase by structural modeling of the intervening residues 665 to 678 (see below).

2Mg 2+ complex in 1IR3 with the AMPPNP in the 2GS7-derived structure, which again appropriately placed the substrate complex in the active site.

Materials and Methods Structural modeling of the active dimeric EGFR A structure of the full-length active dimeric EGFR was created from known structures of the dimeric extracellular domain (3NJP) [17] and individual active (2GS6) and inactive (2GS7) conformation PTK domain structures [4] together assembled in an asymmetric dimer structure.

Publication Year: 2014

A network pharmacology approach to understanding the mechanisms of action of traditional medicine: Bushenhuoxue formula for treatment of chronic kidney disease.

(2014) PLoS One 9

PubMed: 24598793 | PubMedCentral: PMC3943740 | DOI: 10.1371/journal.pone.0089123

Protein Targets Name Gene Symbol PDB-ID Positive Drugs Cutoff Value No a Known target proteins Carbonic anhydrase II CA2 1BN3 Topiramate −8.4 10 Raf kinase RAF1 1C1Y Sorafenib −9.6 12 ... acrophage migration inhibitory factor MIF 1GCZ ethyl 7-hydroxy-2-oxochromene-3-carboxylate −8.9 10 Hepatocyte growth factor HGF 1GMO N,O6-Disulfo-Glucosamine −7 79 Hypoxia-inducible factor 1α HIF1A 1H2K Everolimus −6.3 66 Soluble epoxide hydrolase EPHX2 1ZD3 4-{[(cyclohexylamino)carbonyl]amino} butanoic acid −7.4 15 Carbonic anhydrase XII CA12 1JD0 Hydrochlorothiazide −6.9 26 Peroxisome proliferator-activated receptor PPARG 1K74 Fenofibrate −9.4 39 Angiotensin converting enzyme ACE 1O86 Candoxatril −9 74 Monoamine oxidase B MAOB 1OJ9 Pargyline −9.2 39 Mitogen-activated protein kinase 1 MAPK1 1PME 4-[4-(4-fluorophenyl)-2-[4-[(S)-methylsulfinyl]phenyl]-1H-imidazol-5-yl] pyridine −9.4 27 Mast stem cell growth factor receptor KIT 1T46 Sorafenib −10.1 34 Thymidine phosphorylase TYMP 1UOU Chloro-6-[(2-Iminopyrrolidin-1-Yl)Methyl]Pyrimidine-2,4(1 h,3 h)-Dione −7.7 76 Macrophage metalloelastase MMP12 1UTT (6R)-4-benzyl-6-(1-methyl-2,2-dioxido-1,3-dihydro-2,1-benzisothiazol-5-yl)morpholin-3-one −10.6 6 β2 adrenergic receptor ADRB2 3D4S Carvedilol −9.3 45 Adenosine A2α receptor ADORA2A 3EML Mefloquine −9.8 71 C-C chemokine receptor type 1 CCR1 1Y5D Maraviroc −8.2 35 Mitogen-activated protein kinase 14 MAPK14 1ZZ2 N-[(3z)-5-Tert-Butyl-2-Phenyl-1,2-Dihydro-3h-Pyrazol-3-Ylidene]-N ′ -(4-Chlorophenyl)Urea −8.4 14 Lymphocyte function-associated antigen ITGAL 1CQP Lovastatin −7.2 0 Vasopressin V1α receptor AVPR1A 1YTV Conivaptan −10.5 20 Placeta growth factor PGF 1FZV Suplatast tosylate −5 25 Transforming growth factor beta 1 TGFB1 1KLD NO ligand Tumor necrosis factor ligand superfamily member 5 TNFSF5 1I9R NO ligand Nuclear factor NF-κB NFKB1 1NFI NO ligand Carbonic anhydrase IV CA4 1ZNC NO ligand C-C motif chemokine-2 CCL2/MCP1 2BDN NO ligand DNA-directed RNA polymerase II 19 kDa polypeptide POLR2D 2C35 NO ligand Carbonic anhydrase IX CA9 2HKF NO ligand Known target proteins Plasminogen activator inhibitor-1 SERPINE1 1OC0 NO ligand RAC-α serine/threonine kinase No symbol 1AO2 NO ligand Protein-glutamine γ-glutamyltransferase TGM2 2Q3Z NO ligand Putative targets Tyrosine-protein kinase BTK BTK 3OCS Staurosporine −9.6 53 Small inducible cytokine A5 CCL5 1U4M Heparin_Disaccharide_I-S −6 15 Epidermal growth factor receptor EGFR 2GS7 Flavopiridol −9 19 Estrogen receptor ESR1 3Q97 Estradiol −10 1 Heat shock cognate 71 kDa protein HSPA8 3FZK (2R,3R,4S,5R)-2-[6-amino-8-[(3,4-dichlorophenyl)methylamino]purin-9-yl]-5-(hydroxymethyl)oxolane-3,4-diol −8.2 34 Insulin receptor INSR 2HR7 Hydrochloride) −9.5 21 Proto-oncogene tyrosine-protein kinase LCK LCK 3AC1 N-(2-chloro-6-methylphenyl)-8-[(3S)-3-methylpiperazin-1-yl]imidazo[1,5-a]quinoxalin-4-amine −8.2 60 Hepatocyte nuclear factor 4-alpha HNF4A 1PZL 1_methyl_2-nitro_benzo[e]benzofuran −7.4 79 Glucocorticoid receptor NR3C1 3K22 Flunisolide −10 26 Phosphatidylinositol-4,5-bisphosphate 3-kinase catalytic subunit alpha isoform PIK3CA 3HHM Wortmannin −9.1 20 Plasminogen activator, tissue PLAT 1A5H Iloprost −8.5 87 Acyl-CoA dehydrogenase family member 8, mitochondrial ACTN1 1RX0 Methacrylyl-Coenzyme_A −9 16 Protein tyrosine phosphatase PTPN1 1BZH (Oxalyl-Amino)-Naphthalene-2-Carboxylic_Acid −8 19 Protein kinase C, beta PRKCB 2I0E Vitamin_E −9.7 13 E3 ubiquitin protein ligase VHL 3ZRC 4-((naphthalen-2-ylamino)methyl)benzene-1,2-diol −7.7 21 FYN oncogene related to SRC, FGR, YES FYN 1AOT 2,5,8,11-Tetraoxadodecane −6.6 29 9-mer from C-C chemokine receptor type 5 CCR5 2RLL NO ligand Fc fragment of IgG, low affinity IIb, receptor (CD32) FCGR2B 2FCB NO ligand Fibronectin 1 FN1 3MQL NO ligand Myeloma immunoglobulin D lambda IGHG1 1ZVO NO ligand Solute carrier family 4 SLC4A1 1BTT NO ligand Signal transducer and activator of transcription STAT1 1BF5 NO ligand Jun proto-oncogene JUN 1FOS NO ligand KIAA0101 KIAA0101 No PDB data Catechol-O-methyltransferase COMT No PDB data Protein Targets Name Gene Symbol PDB-ID Positive Drugs Cutoff Value No Putative targets Decorin DCN No PDB data Clusterin CLU No PDB data Transforming growth factor, beta receptor 1 TGFBR1 No PDB data Interleukin 8 IL8 No PDB data Apolipoprotein A–I APOA1 No PDB data Signal transducer and activator of transcription 5B STAT5B No PDB data No a : The number of effective molecular docking.

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

(b) The inactive structures of EGFR (pdb 1XKK, 2GS7), Her2 (pdb id 3PP0, 3RCD), Her3 (pdb id 3LMG,3KEX), Her4 (pdb id 2R4B, 3BBT, 3BCE), Tyk2 (pdb id 3NYX), Tie2 (pdb 2OSC), Met (pdb 2G15), Ron (pdb 3... LS), and Mer kinases (pdb id 2P0C).

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

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

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 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).

The inactive EGFR crystal structures included the following pdb entries: pdb id 2GS7 (Cdk/Src-IF1 EGFR-WT in complex with AMP-PNP); pdb id 1XKK (Cdk/Src-IF1, EGFR-WT in complex with Lapatinib); pdb id 2RFE (Cdk/Src-IF1, EGFR-WT in complex with a 40-residue MIG peptide); pdb id 2RF9 (Cdk/Src-IF2, EGFR-WT in complex with a 60-residue MIG6 peptide); pdb id 4I20 (Cdk/Src-IF2, Apo EGFR-L858R, V948R); pdb id 4I1Z (Cdk/Src-IF2, Apo EGFR-L858R/T790M, V948R); and pdb id 4I21(Cdk/Src-IF2,EGFR-L858R/T790M in complex with MIG6).

Publication Year: 2014