Primary Citation PubMed: 21454582
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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
HER2 (PDB ID: 3PP0) and HER3 (PDB ID: 3KEX) structures were obtained from PDB as well.
Publication Year: 2013
Centrosomal kinase Nek2 cooperates with oncogenic pathways to promote metastasis.
(2013) Oncogenesis 2
PubMed: 24018644 | PubMedCentral: PMC3816224 | DOI: 10.1038/oncsis.2013.34
Figure 6 ( a ) Superimposition of Nek2 (PDB ID: 2JAV), EGFR (PDB ID: 2JIV) and HER2 (PDB ID: 3PP0) kinases.
While the sequence alignments of Nek2 (PDB ID: 2JAV) 14 with that of EGFR (PDB ID: 2JIV) 28 and HER2 (PDB ID: 3PP0) 29 revealed only 22% sequence identity (45% sequence similarity) and 27% sequence identity (49% sequence similarity), respectively, the tertiary folds were remarkably similar ( Figure 6a and Supplementary Figure S1 ).
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).
Publication Year: 2014
Computational analyses of curcuminoid analogs against kinase domain of HER2.
(2014) BMC Bioinformatics 15
PubMed: 25089037 | PubMedCentral: PMC4143557 | DOI: 10.1186/1471-2105-15-261
The preparation of protein The atomic coordinate of HER2 tyrosine kinase domain (HER2-TK) was obtained from the crystallographic structure, accession no. 3PP0 in Protein Data Bank (PDB) [ 7 ].
Recently, in 2011, the first HER2-TK structure complex with pyrimidine compound SYR was released (PDB access 3PP0), providing the new understanding of the kinase structure [ 7 ].
Table 1 Two dimensional structures of curcumin analogs and its Gscore Code Structure Dock score Ref AS-KTC001 -8.35 [ 21 , 22 , 25 ] AS-KTC002 -8.17 [ 21 , 22 , 25 ] AS-KTC003 -8.79 [ 21 , 22 , 25 ] AS-KTC004 -8.24 [ 21 , 22 , 25 ] AS-KTC005 -8.65 [ 21 , 22 , 25 ] AS-KTC006 -8.18 [ 21 , 22 , 25 ] AS-KTC007 -8.20 [ 21 , 22 ] AS-KTC008 -6.40 [ 21 , 22 ] AS-KTC009 -8.66 [ 21 , 22 ] AS-KTC010 -9.03 [ 21 , 22 ] AS-KTC011 -9.26 [ 21 , 22 ] AS-KTC012 -8.56 [ 21 ] AS-KTC013 -8.24 [ 22 ] AS-KTC014 -8.10 [ 22 ] AS-KTC015 -7.71 [ 22 ] AS-KTC016 -7.82 [ 22 ] AS-KTC017 -8.61 [ 22 ] AS-KTC018 -8.04 [ 22 ] AS-KTC019 -8.67 [ 22 ] AS-KTC020 -7.76 [ 22 ] AS-KTC021 -7.12 [ 22 ] AS-KTC022 -7.14 [ 22 ] AS-KTC023 -7.35 [ 22 ] AS-KTC024 -7.33 [ 22 ] Figure 2 The illustration of A) two dimensional (2D) structure and B) three dimensional (3D) structure of SYR from the x-ray structure 3PP0, while panel C) and D) present 2D and 3D structures of curcumin analogs in the binding pocket of HER2-TK from the docking results.
As mention in the previous section, the x-ray crystal structure of HER2-TK, 3PP0 has been used as the model reference template of this study.
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 Cdk/Src-IF3 ErbB2-WT conformation (in blue), DFG-in/αC-helix-out, A-loop open (pdb id 3PP0); Cdk/Src-IF1 ErbB3-WT conformation (in red), DFG... in/αC-helix-out, A-loop closed (pdb id 3KEX, 3LMG); and Cdk/Src-IF1 ErbB4-WT conformation (in green), DFG-in/αC-helix-out, A-loop closed (pdb id 3BBT).
(D) The computed B-factors obtained from simulations of Cdk/Src-IF3 ErbB2-WT structure (pdb id 3PP0, in blue), Cdk/Src-IF1 ErbB3-WT structure (pdb id 3LMG, in red), Cdk/Src-IF1 ErbB4-WT structure (pdb id 3BBT, in green), and the active ErbB4-WT structure (pdb id 3BCE, in maroon).
The simulated crystal structures of the ErbB kinases also included the following pdb entries: pdb id 3PP0 (Cdk/Src-IF3 Apo ErbB2-WT); pdb id 3KEX (Cdk/Src-IF1, Apo ErbB3-WT), pdb id 3LMG (Cdk/Src-IF1, ErbB3-WT in complex with AMP-PNP); pdb id 3BBW(Cdk/Src-IF1, Apo ErbB4-WT); pdb id 3BBT (Cdk/Src-IF1, ErbB4-WT in complex with Lapatinib); and pdb id 3BCE (active, Apo ErbB4-WT).
Kinase Domain EGFR ErbB2 ErbB3 ErbB4 P-loop GSGAFG 719–724 727–732 697–702 700–705 Catalytic K K745 K753 K723 K726 Catalytic αC-E E762 E770 H740 E743 αC-helix 751–769 760–775 738–747 733–749 Hinge motif 792–796 800–804 770–774 773–777 Gatekeeper residue T790 T798 T768 T771 HRD motif 835-HRD-837 843-HRD-845 813-HRN-815 816-818 A-loop DFG motif 855-DFG-857 863-DFG-888 833-DFG-835 836-DFG-838 P+1 loop WMAPE 880–884 888–892 858–862 861–865 R-spine αC-helix M766 M774 I744 M747 R-spine β4-Strand L777 L785 L755 L758 R-spine F (DFG) F856 F864 F834 F837 R-spine H (HRD) H835 H843 H813 H816 R-spine αF-helix D896 D904 D874 D877 The residue ranges of functional regions in the ErbB kinases are based on the crystal structures of EGFR (pdb id 2ITX), ErbB2 (pdb id 3PP0), ErbB3 (pdb id 3LMG), and ErbB4 (pdb id 3BCE).
PubMed ID is not available.
Published in 2015
(f) to (i), The structures of the kinase domains of ErbB-2 (PDB: 3PP0), ErbB-3 (PDB: 4RIW), IGF-1R (PDB: 1K3A) and c-Met (PDB: 1R1W), respectively.
Potential dimerization partners of EGFR, namely ErbB-2 (PDB: 3PP0) [ 68 ], IGF-1R (PDB: 1K3A) [ 69 ] and c-Met (PDB: 1R1W) [ 70 ], were analyzed in our work.
Publication Year: 2015
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