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Fluorine in PDB 2yog: Plasmodium Falciparum Thymidylate Kinase in Complex with A (Thio)Urea-Alpha-Deoxythymidine Inhibitor

Enzymatic activity of Plasmodium Falciparum Thymidylate Kinase in Complex with A (Thio)Urea-Alpha-Deoxythymidine Inhibitor

All present enzymatic activity of Plasmodium Falciparum Thymidylate Kinase in Complex with A (Thio)Urea-Alpha-Deoxythymidine Inhibitor:
2.7.4.9;

Protein crystallography data

The structure of Plasmodium Falciparum Thymidylate Kinase in Complex with A (Thio)Urea-Alpha-Deoxythymidine Inhibitor, PDB code: 2yog was solved by C.Huaqing, J.Carrero-Lerida, A.P.G.Silva, J.L.Whittingham, J.A.Brannigan, L.M.Ruiz-Perez, K.D.Read, K.S.Wilson, D.Gonzalez-Pacanowska, I.H.Gilbert, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 23.37 / 1.50
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 49.060, 58.790, 71.710, 90.00, 95.78, 90.00
R / Rfree (%) 18.233 / 23.262

Other elements in 2yog:

The structure of Plasmodium Falciparum Thymidylate Kinase in Complex with A (Thio)Urea-Alpha-Deoxythymidine Inhibitor also contains other interesting chemical elements:

Chlorine (Cl) 2 atoms

Fluorine Binding Sites:

The binding sites of Fluorine atom in the Plasmodium Falciparum Thymidylate Kinase in Complex with A (Thio)Urea-Alpha-Deoxythymidine Inhibitor (pdb code 2yog). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 6 binding sites of Fluorine where determined in the Plasmodium Falciparum Thymidylate Kinase in Complex with A (Thio)Urea-Alpha-Deoxythymidine Inhibitor, PDB code: 2yog:
Jump to Fluorine binding site number: 1; 2; 3; 4; 5; 6;

Fluorine binding site 1 out of 6 in 2yog

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Fluorine binding site 1 out of 6 in the Plasmodium Falciparum Thymidylate Kinase in Complex with A (Thio)Urea-Alpha-Deoxythymidine Inhibitor


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of Plasmodium Falciparum Thymidylate Kinase in Complex with A (Thio)Urea-Alpha-Deoxythymidine Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F211

b:42.1
occ:0.50
 FAG A:74X211 0.0 42.1 0.5
CBE A:74X211 1.3 41.5 0.5
FAH A:74X211 2.1 42.3 0.5
FAF A:74X211 2.2 42.0 0.5
CAX A:74X211 2.4 41.1 0.5
CAW A:74X211 3.1 41.5 0.5
CLA A:74X211 3.3 44.0 0.5
CAL A:74X211 3.4 39.4 0.5
CAK A:74X211 4.4 40.9 0.5
CG A:LYS60 4.4 26.8 0.5
CG A:LYS60 4.5 26.7 0.5
CE A:LYS60 4.5 28.4 0.5
CE A:LYS60 4.6 28.8 0.5
CAV A:74X211 4.6 38.4 1.0
O A:HOH2075 4.8 43.2 1.0
CAJ A:74X211 5.0 39.6 0.5

Fluorine binding site 2 out of 6 in 2yog

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Fluorine binding site 2 out of 6 in the Plasmodium Falciparum Thymidylate Kinase in Complex with A (Thio)Urea-Alpha-Deoxythymidine Inhibitor


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of Plasmodium Falciparum Thymidylate Kinase in Complex with A (Thio)Urea-Alpha-Deoxythymidine Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F211

b:42.3
occ:0.50
 FAH A:74X211 0.0 42.3 0.5
CBE A:74X211 1.3 41.5 0.5
FAG A:74X211 2.1 42.1 0.5
FAF A:74X211 2.2 42.0 0.5
CAX A:74X211 2.3 41.1 0.5
CAL A:74X211 2.6 39.4 0.5
O A:HOH2075 3.4 43.2 1.0
CAW A:74X211 3.7 41.5 0.5
CB A:LEU59 3.8 20.4 1.0
CD1 A:LEU59 3.9 19.1 1.0
CAV A:74X211 4.0 38.4 1.0
CLA A:74X211 4.5 44.0 0.5
CG A:LEU59 4.5 20.4 1.0
O A:HOH2220 4.6 22.7 1.0
CAK A:74X211 4.7 40.9 0.5
NAQ A:74X211 4.8 34.7 1.0
CAJ A:74X211 4.9 39.6 0.5

Fluorine binding site 3 out of 6 in 2yog

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Fluorine binding site 3 out of 6 in the Plasmodium Falciparum Thymidylate Kinase in Complex with A (Thio)Urea-Alpha-Deoxythymidine Inhibitor


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of Plasmodium Falciparum Thymidylate Kinase in Complex with A (Thio)Urea-Alpha-Deoxythymidine Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F211

b:42.0
occ:0.50
 FAF A:74X211 0.0 42.0 0.5
CBE A:74X211 1.3 41.5 0.5
FAH A:74X211 2.2 42.3 0.5
FAG A:74X211 2.2 42.1 0.5
CAX A:74X211 2.4 41.1 0.5
CAW A:74X211 3.0 41.5 0.5
CLA A:74X211 3.0 44.0 0.5
CG A:LYS60 3.3 26.7 0.5
CG A:LYS60 3.3 26.8 0.5
CB A:LEU59 3.4 20.4 1.0
CAL A:74X211 3.5 39.4 0.5
C A:LEU59 3.6 23.6 1.0
N A:LYS60 3.7 24.5 1.0
O A:LEU59 3.8 23.9 1.0
CA A:LYS60 4.1 25.9 0.5
CA A:LYS60 4.1 25.9 0.5
CA A:LEU59 4.1 21.8 1.0
O A:SER56 4.2 19.5 1.0
CB A:LYS60 4.3 25.6 0.5
CB A:LYS60 4.3 25.6 0.5
CAK A:74X211 4.3 40.9 0.5
CE A:LYS60 4.4 28.8 0.5
CD A:LYS60 4.5 28.2 0.5
CD A:LYS60 4.5 27.9 0.5
CE A:LYS60 4.6 28.4 0.5
CAV A:74X211 4.6 38.4 1.0
CG A:LEU59 4.7 20.4 1.0
CD1 A:LEU59 4.8 19.1 1.0
O A:HOH2075 4.9 43.2 1.0
CAJ A:74X211 5.0 39.6 0.5

Fluorine binding site 4 out of 6 in 2yog

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Fluorine binding site 4 out of 6 in the Plasmodium Falciparum Thymidylate Kinase in Complex with A (Thio)Urea-Alpha-Deoxythymidine Inhibitor


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 4 of Plasmodium Falciparum Thymidylate Kinase in Complex with A (Thio)Urea-Alpha-Deoxythymidine Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F211

b:23.5
occ:1.00
 FAG B:74X211 0.0 23.5 1.0
CBE B:74X211 1.3 24.9 1.0
FAH B:74X211 2.1 26.9 1.0
FAF B:74X211 2.2 25.5 1.0
CAX B:74X211 2.4 25.8 1.0
CAW B:74X211 3.0 28.9 1.0
CLA B:74X211 3.0 34.2 1.0
CG B:LYS60 3.3 18.5 1.0
CB B:LEU59 3.3 14.2 1.0
CAL B:74X211 3.5 23.4 1.0
N B:LYS60 3.8 15.9 1.0
O B:SER56 3.8 16.9 1.0
C B:LEU59 3.9 15.4 1.0
CE B:LYS60 3.9 24.5 1.0
CA B:LEU59 4.2 14.3 1.0
NH1 B:ARG47 4.2 23.1 1.0
CD B:LYS60 4.3 21.6 1.0
OG B:SER56 4.3 17.8 1.0
CA B:LYS60 4.3 17.5 1.0
O B:LEU59 4.3 16.2 1.0
CB B:LYS60 4.3 16.8 1.0
CAK B:74X211 4.3 30.7 1.0
CD1 B:LEU59 4.4 16.3 1.0
CG B:LEU59 4.5 13.8 1.0
CD B:ARG47 4.6 20.2 1.0
CA B:SER56 4.7 14.7 1.0
C B:SER56 4.7 15.6 1.0
CAV B:74X211 4.7 25.9 1.0
CZ B:ARG47 4.8 23.3 1.0
NE B:ARG47 4.9 22.1 1.0
N B:LEU59 5.0 14.1 1.0

Fluorine binding site 5 out of 6 in 2yog

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Fluorine binding site 5 out of 6 in the Plasmodium Falciparum Thymidylate Kinase in Complex with A (Thio)Urea-Alpha-Deoxythymidine Inhibitor


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 5 of Plasmodium Falciparum Thymidylate Kinase in Complex with A (Thio)Urea-Alpha-Deoxythymidine Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F211

b:26.9
occ:1.00
 FAH B:74X211 0.0 26.9 1.0
CBE B:74X211 1.3 24.9 1.0
FAG B:74X211 2.1 23.5 1.0
FAF B:74X211 2.2 25.5 1.0
CAX B:74X211 2.4 25.8 1.0
CAW B:74X211 3.0 28.9 1.0
CLA B:74X211 3.1 34.2 1.0
CAL B:74X211 3.4 23.4 1.0
NH1 B:ARG47 3.6 23.1 1.0
CZ B:ARG47 4.0 23.3 1.0
CE B:LYS60 4.0 24.5 1.0
CG B:LYS60 4.3 18.5 1.0
CAK B:74X211 4.3 30.7 1.0
NH2 B:ARG47 4.4 24.6 1.0
NE B:ARG47 4.5 22.1 1.0
CAV B:74X211 4.6 25.9 1.0
CD B:LYS60 4.8 21.6 1.0
CD B:ARG47 4.8 20.2 1.0
CAJ B:74X211 5.0 28.6 1.0

Fluorine binding site 6 out of 6 in 2yog

Go back to Fluorine Binding Sites List in 2yog
Fluorine binding site 6 out of 6 in the Plasmodium Falciparum Thymidylate Kinase in Complex with A (Thio)Urea-Alpha-Deoxythymidine Inhibitor


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 6 of Plasmodium Falciparum Thymidylate Kinase in Complex with A (Thio)Urea-Alpha-Deoxythymidine Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F211

b:25.5
occ:1.00
 FAF B:74X211 0.0 25.5 1.0
CBE B:74X211 1.3 24.9 1.0
FAH B:74X211 2.2 26.9 1.0
FAG B:74X211 2.2 23.5 1.0
CAX B:74X211 2.4 25.8 1.0
CAL B:74X211 2.8 23.4 1.0
CD B:ARG47 3.3 20.2 1.0
NE B:ARG47 3.3 22.1 1.0
CZ B:ARG47 3.5 23.3 1.0
NH1 B:ARG47 3.5 23.1 1.0
CAW B:74X211 3.7 28.9 1.0
CD1 B:LEU59 3.8 16.3 1.0
CB B:LEU59 4.1 14.2 1.0
CAV B:74X211 4.1 25.9 1.0
O B:HOH2213 4.2 16.2 1.0
NH2 B:ARG47 4.2 24.6 1.0
CLA B:74X211 4.4 34.2 1.0
CG B:LEU59 4.6 13.8 1.0
CG B:ARG47 4.8 17.4 1.0
OG B:SER56 4.8 17.8 1.0
CAK B:74X211 4.8 30.7 1.0
NAQ B:74X211 4.8 22.8 1.0

Reference:

H.Cui, J.Carrero-Lerida, A.P.G.Silva, J.L.Whittingham, J.A.Brannigan, L.M.Ruiz-Perez, K.D.Read, K.S.Wilson, D.Gonzalez-Pacanowska, I.H.Gilbert. Synthesis and Evaluation of Alpha-Thymidine Analogues As Novel Antimalarials. J.Med.Chem. V. 55 10948 2012.
ISSN: ISSN 0022-2623
PubMed: 23240776
DOI: 10.1021/JM301328H
Page generated: Mon Jul 14 15:02:22 2025

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