Citations in PubMed

Primary Citation PubMed: 11071809 Citations in PubMed

PDB ID Mentions in PubMed Central Article count: 2

Citations in PubMed

This linkout lists citations, indexed by PubMed, to the Primary Citation for this PDB ID.

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.

  • 3 per page
  • 5 per page
  • 10 per page
  • view all
  • Publication Year
  • Ascending
  • Descending

Design of Thymidine Analogues Targeting Thymidilate Kinase of Mycobacterium tuberculosis.

(2013) Tuberc Res Treat 2013

PubMed: 23634301 | PubMedCentral: PMC3619541 | DOI: 10.1155/2013/670836

About this additional HB with Tyr39 it is interesting to point out, among the few differences of the binding sites of TMPK mt and TMPK h (the human corresponding enzyme-PDB code 1E99) where Arg14, Tyr... 9 and Asn100 are replaced in the last one by Ser20, Arg45 and Gly102, respectively [ 41 ], the crucial opportunity to exploit this structural and functional difference (interaction with Tyr39) to design selective inhibitors for TMPK mt .

Publication Year: 2013


LigSearch: a knowledge-based web server to identify likely ligands for a protein target.

(2013) Acta Crystallogr D Biol Crystallogr 69

PubMed: 24311580 | PubMedCentral: PMC3852652 | DOI: 10.1107/S0907444913022294

It compares the protein–ligand interactions for the same 3′-azido-3′-deoxy­thymidine 5′-monophosphate ligand bound to S. aureus thymidylate synthase in PDB entr... 4eaq and human thymidyl­ate synthase in PDB entry 1e99 .

Candidate compound LigSearch PDB code (chain) Score Sequence identity (%) LigSearch cluster 1   P 1 -(5′-Adenosyl)- P 5 -(5′-thymidyl)pentaphosphate (Fig. 4 ▶ a ) T5A 4tmk ( A ) 29/33 34.0   P 1 -(5′-Adenosyl)- P 5 -[5′-(3′-azido-3′-deoxythymidyl)] pentaphosphate Z5A 5tmp ( A ) 25/29 34.0  Phosphoaminophosphonic acid adenylate ester ANP 1nmy ( A ) 23/30 22.6   Adenosine 5′-diphosphate ADP 2cdn ( A ) 23/32 24.3   Adenosine 5′-triphosphate ATP 1e2q ( A ) 18/27 22.6   2′-Deoxyguanosine 5′-triphosphate DGT 2vp2 ( A ) 18/38 26.2   Guanosine 5′-monophosphate 5GP 1ex7 7/– 23.7 LigSearch cluster 3   Thymidine 5′-diphosphate (Fig. 4 ▶ b ) TYD 3hjn ( A ) 24/27 41.8   Thymidine 5′-phosphate † TMP 2ccg ( A ) 21/21 100.0  Thymidine 5′-triphosphate TTP 2vp0 ( A ) 21/37 26.2  2′-Deoxycytidine 5′-triphosphate DCP 2vp4 ( A ) 20/34 26.2   Thymidine THM 4esh ( A ) 13/15 35.9  3′-Deoxythymidine 5′-monophosphate 2DT 1nn0 ( A ) 11/14 22.6   3′-Azido-3′-deoxythymidine 5′-monophosphate ‡ ATM 1e99 ( A ) 11/19 22.6  3′-Fluoro-3′-deoxythymidine monophosphate FDM 1nmx ( A ) 11/14 22.6   2′-Deoxycytidine DCZ 1j90 ( A ) 10/22 22.7   ( E )-5-(2-Bromovinyl)-2′-deoxyuridine 5′-monophosphate BVP 2w0s ( A ) 8/12 25.3  5-Hydroxymethyluridine 2′-deoxy-5′-monophosphate 5HU 1mrs ( A ) 8/15 28.6  3′-Deoxy-3′-aminothymidine monophosphate NYM 1nmz ( A ) 8/15 22.6  2′,3′-Dideoxycytidine 5′-monophosphate DOC 2vp9 ( A ) 6/20 25.8  5-Bromovinyldeoxyuridine BVD 2vqs ( A ) 5/11 26.8   Gemcitabine GEO 2vpp ( A ) 5/17 26.7   5-Fluorouridine 5′-monophosphate 5FU 2vp6 ( A ) 5/19 25.8 LigSearch cluster 15  4-(2-Hydroxyethyl)-1-piperazineethanesulfonic acid (Fig. 4 ▶ c ) EPE 2plr ( A ) 6/9 28.3 Not found by LigSearch   3′-Azido-3′-deoxythymidine — — — —  Diphosphate — — — — † Structure solved as PDB entry 4dwj .

Figure 5 A schematic diagram of the protein–ligand interactions in two distantly related proteins: ( a ) thymidylate synthase from S. aureus (PDB entry 4eaq ) and ( b ) human thymidylate synthase (PDB entry 1e99 ).

Publication Year: 2013