Primary Citation PubMed: 21163962
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Modulation of epigenetic targets for anticancer therapy: clinicopathological relevance, structural data and drug discovery perspectives.
(2013) Curr Pharm Des 19
PubMed: 23016851 | PubMedCentral: PMC3529403 | DOI: null
Available Three-dimensional Structures of Mammals DNMTs Name Organism PDB ID Ligand Domain References DNMT1 Mus musculus 3AV4 DNMT1 3AV5 SAH DNMT1 3AV6 SAM DNMT1 3PT6 DNA, SAH DNMT1 [ 414 ] ... PT9 SAH DNMT1 and DNA complex Homo sapiens 3EPZ RFTS domain, Beta-d-glucose DNMT1 [ 415 ] 3PTA DNA, SAH RFTS [ 414 ] 3SWR Sinefungin, MES a , DNMT1 and DNA complex 3OS5 SETD7, SAH DNMT1 [ 386 ] DNMT2 Homo sapiens 1G55 SAH Complex with SETD7 [ 412 ] DNMT3A Homo sapiens 2QRV DMNT2 (deleted in 191-237) [ 416 ] 3A1A DNMT3a-DNMT3L C-terminal complex [ 417 ] 3A1B ADD and histone H3 complex 3LLR ADD and histone H3 complex [ 418 ] DNMT3B Mus musculus 1KHC PWWP [ 419 ] Homo sapiens 3FLG PWWP 3QKJ PWWP [ 418 ] DNMT3L Homo sapiens 2PV0 PWWP [ 420 ] 2PVC Histone H3 peptide DNMT3L 2QRV SAH DNMT3L - DNMT3a C-terminal complex [ 416 ] a ligand PDB ID Table 7.
Publication Year: 2013
Molecular modeling studies of the novel inhibitors of DNA methyltransferases SGI-1027 and CBC12: implications for the mechanism of inhibition of DNMTs.
(2013) PLoS One 8
PubMed: 23637988 | PubMedCentral: PMC3636198 | DOI: 10.1371/journal.pone.0062152
The structure bound with SAH and DNA containing unmethylated CpG sites was revealed first with a resolution of 3.6 Å (PDB id: 3PTA)  .
ZF-CxxC domain-containing proteins, CpG islands and the chromatin connection.
(2013) Biochem Soc Trans 41
PubMed: 23697932 | PubMedCentral: PMC3685328 | DOI: 10.1042/BST20130028
Figure 3 Structural insight into the DNA-binding properties of ZF-CxxC proteins ( A and B ) Crystal structures of the ( A ) Homo sapiens DNMT1 (PDB code 3PTA) and ( B ) Xenopus tropicalis TET3 (PDB co... e 4HP3) ZF-CxxC domains in complex with DNA, viewed down the double-helix axis (left) and rotated 60° to the right (right).
( C ) A manually curated multiple sequence alignment of the amino acid sequence of four ZF-CxxC structures (PDB codes: CFP1, 3QMG; DNMT1, 3PTA; MLL, 2KKF; TET3, 4HP3).
Selective non-nucleoside inhibitors of human DNA methyltransferases active in cancer including in cancer stem cells.
(2014) J Med Chem 57
PubMed: 24387159 | PubMedCentral: PMC3983372 | DOI: 10.1021/jm4012627
Then, the Glide program of the Schrödinger package 33 was used to dock these compounds into the two selected DNMT1 X-ray structures (PDB 3SWR, Hashimoto and Cheng, unpublished data, and PDB 3P... A( 32 )).
In particular, compound 5 was docked in two different DNMT1 structures available in the Protein Data Bank (PDB): DNMT1 (residues 600–1600) crystallized in complex with sinefungin (PDB 3SWR, Hashimoto and Cheng, unpublished data) and DNMT1 (residues 646–1600) in complex with both AdoHcy and a 19 bp DNA duplex (PDB 3PTA).
In this respect, the DNMT1 structures (PDB 3PTA and 3SWR) were also searched for different binding sites with the SiteMap software available within the Maestro suite.
Publication Year: 2014
PubMed ID is not available.
Published in 2015
The crystal structures of the human DNMT1 RFTS domain (residues 351–597, PDB ID: 3EPZ; Syeda et al., 2011 ), human DNMT1 CXXC, nBAH/cBAH, and catalytic domains bound to DNA-containing unmethyl... ted CpG sites (residues 646–1600, PDB ID: 3PTA; Song et al., 2011 ), human DNMT2 catalytic domain (residues 1–188 and 248–391, PDB ID: 1G55; Dong et al., 2001 ), human DNMT3A PWWP (residues 275–427, PDB ID: 3LLR), and ADD domains (residues 476–614, PDB ID: 3A1A; Otani et al., 2009 ; Wu et al., 2011 , respectively), human DNMT3B PWWP domain (residues 293–442; PDB ID: 3QKJ; Wu et al., 2011 ), human DNMT3L ADD domain (residues 34–277 and 279–380, PDB ID: 2PV0; Ooi et al., 2007 ), are shown.
Publication Year: 2015
A structural comparison indicates that DNMT1 in the complex structure adopts a similar fold to that in DNMT1-DNA structure (PDB 3PTA) 27 , with a root-mean-square deviation of 0.97 Å f... r 802 aligned Cα atoms ( Supplementary Fig. 2b ).
Published in 2014
Recently, the crystal structure of the murine catalytic complex Dnmt3A/3L (PDB: 2QRV[ 9 ]) and several crystal structures of DNMT1 have been published (PDB: 3PTA,[ 10 ] 3OS5, 4DA4[ 11 ] and 3PT6[ 10 ]... , together with molecular docking and pharmacophore modelling studies based on these structures.
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