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PDB ID Mentions in PubMed Central Article count: 4

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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Heterologous expression of plasmodial proteins for structural studies and functional annotation.

(2008) Malar J 7

PubMed: 18828893 | PubMedCentral: PMC2567985 | DOI: 10.1186/1475-2875-7-197

PlasmoDB annotation Product Drug-ability Index (max is 1) MM (Da) pI Heterologous Expression (Ref) Tag Special conditions (e.g. codon adaptation, TM, trunctions) Structure (PDB code) PF14_0053 Ribonuc... eotide reductase small subunit 1 40600 5.2 E. coli [ 212 ] His and GST - - PFD0830w Bifunctional dihydrofolate reductase-thymidylate synthase 1 71738 7.2 - E. coli (various) - S. cerevisiae (complemeted) (various) - Cell free systems [ 207 ] - - Purposely truncated versions or domains - Codon optimised - S. cerevisiae adapted 1J3I 1J3J 1J3K PFE0520c Topoisomerase I 1 98110 9.8 - - - - PFF0160c Dihydroorotate dehydrogenase, mitochondrial precursor 1 65559 9.4 E. coli [ 213 ] His N-terminally truncated pRIL tRNA additions 1TV5 PFI1020c Inosine-5'-monophosphate dehydrogenase 1 56151 8.0 - - - - PF11_0377 Casein kinase 1 0.9 37631 9.7 E. coli [ 214 ] His 1lhx PF14_0192 Glutathione reductase 0.9 56679 8.1 E. coli complementation [ 215 ] His Gene complementation 1ONF PFI1685w cAMP-dependent protein kinase catalytic subunit 0.9 40197 9.1 - - - - PFI1170c Thioredoxin reductase 0.9 59687 7.8 E. coli [ 216 ] His - - MAL13P1.279 Protein kinase 5 0.9 32997 8.0 E. coli [ 217 ] His pRIL tRNA addition 1OB3 PFC0525c Glycogen synthase kinase 3 0.9 51616 5.2 E. coli [ 218 ] V5/His-/thioredoxin - - PFL2250c Rac-beta serine/threonine kinase 0.9 88096 10 E. coli [ 219 ] His or GST pRIL tRNA addition - PF10_0121 Hypoxanthine phosphoribosyltransferase 0.8 70076 4.6 E. coli [ 220 ] - - 1CJB PF10_0165 DNA polymerase delta catalytic subunit 0.8 127072 8.7 E. coli [ 221 ] 3-galactosidase - - PF10_0322 S-adenosylmethionine decarboxylase-ornithine decarboxylase 0.8 168171 6.3 E. coli [ 222 ] STREP - - PF13_0141 L-lactate dehydrogenase 0.8 34108 7.6 E. coli [ 223 , 224 ] - - 1 TM/1 signal peptide - 2xYT - reducing cell growth temperature to 15°C 1CEQ PF13_0287 Adenylosuccinate synthetase 0.8 50066 7.7 E. coli [ 225 ] - Low-temperature inductions were carried out at 20°C for 12 h 1P9B PFI1090w S-adenosylmethionine synthetase 0.8 44844 6.7 E. coli [ 226 ] His - PF14_0076 Plasmepsin 1 precursor 0.8 51461 7.2 1 TM 1PFZ PF14_0077 Plasmepsin 2 precursor 0.8 51481 5.3 E. coli [ 227 ] - 1 TM - Solubilised and refolded 1SME PF14_0125 Deoxyhypusine synthase 0.8 57429 6 P. vivax expressed 1 TM - PF14_0127 N-myristoyltransferase 0.8 47971 8.3 E. coli [ 228 ] His - -.

Publication Year: 2008


WISDOM-II: screening against multiple targets implicated in malaria using computational grid infrastructures.

(2009) Malar J 8

PubMed: 19409081 | PubMedCentral: PMC2691744 | DOI: 10.1186/1475-2875-8-88

Table 1 Structural features of the targets used in WISDOM II Target Activity Structure PDB id Resolution Å Cocrystallized Ligand Co-factor Pf GST Detoxification Dimer 1Q4J 2.2 GTX NO Pf DHFR (... ild type) DNA synthesis Polymer 1J3I 2.33 WR99210 NADPH Pf DHFR (Quadruple mutant) DNA synthesis Polymer 1J3K 2.10 WR99210 NADPH Pv DHFR (wild type) DNA synthesis Polymer 2BL9 1.90 Pyrimethamine NADPH P vDHFR (Double mutant) DNA synthesis Polymer 2BLC 2.25 Des- chloropyrimethamine NADPH Target structures Glutathione-S-transferase The P. falciparum glutathione S-transferase enzyme belongs to a super family of multifunctional, dimeric, phase II detoxification enzymes that can bind various xenobiotic, electrophilic substrates.

The results displayed in Table 4 correspond to the quadruple mutant results ( 1J3I : PDB ID) and Table 5 corresponds to the wild type results ( 1J3K : PDB ID).

Plasmodium vivax DHFR (PvDHFR) and Plasmodium falciparum DHFR (PfDHFR) The protein structures used in this investigation are the crystal structures of wild-type P. falciparum DHFR (PDB code 1J3I ) and of its N51I+C59R+S108N+I164L highly resistant mutant (PDB code 1J3K ), both in complex with NADPH and the potent inhibitor WR99210, and the structures of wild type P. vivax DHFR (PDB code 2BL9 ) and of its S58R+S117N resistant mutant (PDB code 2BLC ) in complex with pyrimethamine and des-chloro pyrimethamine, respectively [ 41 , 46 ].

Figure 2 and 3 display the re-docking pose of WR9 against minimized structure of the Pf DHFR (1J3K) and Pf DHFR (1J3I), respectively, on the right hand side of the figure we can see the docking pose (CPK color) and reference co-ordinates in red color (IJ3K) and violet color (1J3I).

Publication Year: 2009


Binding modes of 2,4-diaminoquinazoline and 2,4-diaminopteridine analogs to P. falciparum dihydrofolate reductase enzyme: Molecular docking studies.

(2010) Indian J Pharm Sci 72

PubMed: 21188041 | PubMedCentral: PMC3003165 | DOI: 10.4103/0250-474X.70478

A molecular docking study was carried out on 28 compounds belonging to 2,4-diaminoquinazoline and 2,4-diaminopteridine analogs using Glide, FlexX and GOLD programs and the X-ray crystallographic struc... ures of the quadruple mutant (1J3K:pdb) and wild type (1J3I:pdb) Plasmodium falciparum dihydrofolate reductase enzyme.

Protein structure preparation: The X-ray crystallographic structures of the wild type (1J3I:pdb)[ 24 ] and quadruple mutant Pf DHFR (1J3K:pdb)[ 24 ] enzymes were obtained from the RCSB protein databank.

Publication Year: 2010


Antifolate Agents Against Wild and Mutant Strains of Plasmodium falciparum.

(2014) Indian J Pharm Sci 76

PubMed: 24843184 | PubMedCentral: PMC4023280 | DOI: null

TABLE 1 CHEMICAL STRUCTURE OF SYNTHESISED COMPOUNDS Preparation of protein: The X-ray crystal structures of both wild type and tetramutant forms of pf DHFR with PDB code 1J3I (wild type) and 1J3K (tet... amutant)[ 11 ] were used for the design of new DHFR inhibitors.

The configuration of WR99210 in the crystal structures of pf DHFR (PDB codes 1J3I and 1J3K) was used for an initial alignment of other ligands in the active site (defined by residues enclosed within a 10.0 Å radius from the centroid of WR99210) of the enzyme.

Publication Year: 2014