Primary Citation PubMed: 11071809
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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 ).
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