Citations in PubMed

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PDB ID Mentions in PubMed Central Article count: 12

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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Clinical relevance of KRAS in human cancers.

(2010) J Biomed Biotechnol 2010

PubMed: 20617134 | PubMedCentral: PMC2896632 | DOI: 10.1155/2010/150960

Model of 3GFT molecule was rendered in Swiss-PdbViewer v4.0.1 ( http://spdbv.vital-it.ch/ ).

Publication Year: 2010


Activation of K-RAS by co-mutation of codons 19 and 20 is transforming.

(2011) J Mol Signal 6

PubMed: 21371307 | PubMedCentral: PMC3056876 | DOI: 10.1186/1750-2187-6-2

The shortened K-RAS protein structure used for modelling was obtained from the Protein Data Bank (PDB ID: 3gft ) and visualised using PyMOL ( http://www.pymol.org ).

Publication Year: 2011


The structural impact of cancer-associated missense mutations in oncogenes and tumor suppressors.

(2011) Mol Cancer 10

PubMed: 21575214 | PubMedCentral: PMC3123651 | DOI: 10.1186/1476-4598-10-54

Table 1 Overview of genes Gene name Length (AA) Mut SNP PDB codes (sequence range) Oncogenes AKT1 478 6 5 1UNQ A (1-123), 3CQW A (144-480) BRAF 766 46 3 3D4Q A (433-726), 3NY5 A (153-237) EGFR 1210 22... 9 1YY9 A (25-642), 1XKK A (695-1022) GNAS 394 12 9 1AZS C (1-394) HRAS 189 19 0 4Q21 A (1-189) KIT 976 9 9 2EC8 A (1-519), 3G0E A (544-935) KRAS 188 85 1 3GFT A (1-164) MET 1408 24 30 2UZX B (25-740), 3DKC A (1049-1360) NRAS 189 9 1 3CON A (1-172) PIK3CA 1068 148 17 2RD0 A (1-1068) PTPN11 593 7 6 2SHP A (3-529) RET 1114 24 3 2IVS A (705-1013), 2X2U A (29-270) Tumor Suppressor Genes CDH1 882 17 3 2O72 A (155-367) CDKN2A 156 76 10 1BI7 B (1-156) FBXW7 707 34 4 2OVR B (263-707) MLH1 756 8 3 3NA3 A (1-347) MSH2 934 12 17 2O8B A (1-934) PTEN 403 93 2 1D5R A (8-353) RB1 928 7 9 2R7G A (380-787), 2QDJ A (52-355), 2AZE C (829-874) SMAD4 552 51 3 1DD1 A (285-552) STK11 433 30 1 2WTK C (43-347) TP53 393 826 17 2VUK A (94-312), 1AIE A (326-356) VHL 213 216 16 1LM8 V (54-213) WT1 449 9 3 2PRT A (318-438) Abbreviations: AA, amino acid, Mut, number of mutations, SNP, number of SNPs, PDB, Protein Data Bank Single nucleotide polymorphism dataset ( Snp ) As a control set, we extracted single nucleotide polymorphism (SNP) data for the 24 genes from version 131 of the common variation database dbSNP [ 17 ].

Publication Year: 2011


Novel allosteric sites on Ras for lead generation.

(2011) PLoS One 6

PubMed: 22046245 | PubMedCentral: PMC3201956 | DOI: 10.1371/journal.pone.0025711

AutoDock 4.2 was used to dock the ligands onto the entire surface of the K-Ras crystal structure (PDB code 3GFT) with a grid dimension large enough to cover the entire protein (143×149×... 155 Å, with 0.375 Å grid spacing).

Publication Year: 2011


The role of conserved waters in conformational transitions of Q61H K-ras.

(2012) PLoS Comput Biol 8

PubMed: 22359497 | PubMedCentral: PMC3280954 | DOI: 10.1371/journal.pcbi.1002394

These waters were selected for a more detailed analysis by MD. Molecular dynamics simulations The 2.27 Å resolution crystal structure of GTP-bound Q61H K-ras (PDB id: 3GFT) was used to perform... seven sets of multi-copy MD simulations ( Table 1 ).

Publication Year: 2012


Computational analysis of KRAS mutations: implications for different effects on the KRAS p.G12D and p.G13D mutations.

(2013) PLoS One 8

PubMed: 23437064 | PubMedCentral: PMC3577811 | DOI: 10.1371/journal.pone.0055793

For this study, the (PS) 2 server selected the X-ray crystal structure of the KRAS-GTP complex (PDB ID: 3GFT) through a template consensus strategy [40] as the template structure.

Results Molecular Modeling and Structural Analysis of Human KRAS Human KRAS-GTP models were constructed using the published crystal structure (PDB Id: 3GFT) as the template ( Figure 1 ).

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

iPAC finds additional clusters One example where iPAC finds additional clusters is in the KRAS protein when analyzing the 3GFT structure a [ 21 ].

Tong Y Tempel W Shen L Arrowsmith C Edwards A Sundstrom M Weigelt J Park H Bockharev A Human K-Ras in complex with a GTP analogue 2009 [ http://www.rcsb.org/pdb/explore.do?structureId=3GFT ] Benjamini Y Hochberg Y Controlling the false discovery rate: a practical and powerful approach to multiple testing J R Stat Soc Series B (Methodological) 1995 57 289 300 [ http://www.jstor.org/stable/2346101 ] Dunn OJ Confidence intervals for the means of dependent, normally distributed variables J Am Stat Assoc 1959 54 287 613 621 [ http://www.jstor.org/stable/2282541 ] 10.1080/01621459.1959.10501524 Dunn OJ Multiple comparisons among means J Am Stat Assoc 1961 56 293 52 64 [ http://www.jstor.org/stable/2282330 ] 10.1080/01621459.1961.10482090 Gong Y Kakihara Y Krogan N Greenblatt J Emili A Zhang Z Houry WA An atlas of chaperone-protein interactions in Saccharomyces cerevisiae: implications to protein folding pathways in the cell Mol Syst Biol 2009 5 [ http://www.nature.com/doifinder/10.1038/msb.2009.26 ] Mankoo PK Sukumar S Karchin R PIK3CA somatic mutations in breast cancer: Mechanistic insights from Langevin dynamics simulations Proteins: Struct, Funct, Bioinformatics 2009 75 2 499 508 10.1002/prot.22265 Herbst RS Review of epidermal growth factor receptor biology Int J Radiat Oncol *Biology* Phys 2004 59 2, Supplement S21 S26 [ http://www.sciencedirect.com/science/article/pii/S0360301604003311 ] 10.1016/j.ijrobp.2003.11.041 Scagliotti GV Selvaggi G Novello S Hirsch FR The biology of epidermal growth factor receptor in lung cancer Clin Cancer Res 2004 10 12 4227s 4232s [ http://clincancerres.aacrjournals.org/content/10/12/4227s.abstract ] 10.1158/1078-0432.

Publication Year: 2013


A graph theoretic approach to utilizing protein structure to identify non-random somatic mutations.

(2014) BMC Bioinformatics 15

PubMed: 24669769 | PubMedCentral: PMC4024121 | DOI: 10.1186/1471-2105-15-86

Figure 7 The KRAS structure (PDB ID 3GFT) color coded by region: amino acids 13–22 are blue, 24–60 are red and 62–145 are yellow.

CCR-07-0001 17699853 Pan Q Chanthery Y Liang WC Stawicki S Mak J Rathore N Tong RK Kowalski J Yee SF Pacheco G Ross S Cheng Z Le Couter J Plowman G Peale F Koch AW Wu Y Bagri A Tessier-Lavigne M Watts RJ Blocking neuropilin-1 function has an additive effect with anti-VEGF to inhibit tumor growth Cancer Cell 2007 11 53 67 10.1016/j.ccr.2006.10.018 17222790 Appleton BA Wu P Maloney J Yin J Liang WC Stawicki S Mortara K Bowman KK Elliott JM Desmarais W Bazan JF Bagri A Tessier-Lavigne M Koch AW Wu Y Watts RJ Wiesmann C Structural studies of neuropilin/antibody complexes provide insights into semaphorin and VEGF binding EMBO J 2007 26 23 4902 4912 [PDB ID: 2QQI] 10.1038/sj.emboj.7601906 17989695 Tong Y Tempel W Shen L Arrowsmith C Edwards A Sundstrom M Weigelt J Bockharev A Park H Human K-Ras in complex with a GTP analogue 2009 [ http://www.rcsb.org/pdb/explore.do?structureId=3GFT ] [PDB ID: 3GFT].

Publication Year: 2014


The structural basis for cancer treatment decisions.

(2014) Oncotarget 5

PubMed: 25277176 | PubMedCentral: PMC4202123 | DOI: 10.18632/oncotarget.2439

The crystal structure of GDP-H-Ras/RasGAP complex (PDB code 1WQ1) is remodeled with the GTP-K-Ras crystal structure (PDB code 3GFT).

Publication Year: 2014


Novel KRAS gene mutations in sporadic colorectal cancer.

(2014) PLoS One 9

PubMed: 25412182 | PubMedCentral: PMC4239073 | DOI: 10.1371/journal.pone.0113350

The K-ras protein structure used for modeling was obtained from the Protein Data Bank (PDB ID: 3gft).

Publication Year: 2014


Allosteric modulation of Ras and the PI3K/AKT/mTOR pathway: emerging therapeutic opportunities.

(2014) Front Physiol 5

PubMed: 25566081 | PubMedCentral: PMC4267178 | DOI: 10.3389/fphys.2014.00478

(A) The overall structure of K-Ras shown in ribbon representation (PDB ID: 3GFT) with switch I, switch II, and the p-loop highlighted.

Publication Year: 2014


PubMed ID is not available.

Published in 2015

PubMedCentral: PMC4518475

(F) KRas from PDB: 3GFT overlaid with the ligand from PDB: 4EPY .

Publication Year: 2015