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Chlorine in PDB 2yof: Plasmodium Falciparum Thymidylate Kinase in Complex with A (Thio)Urea-Beta-Deoxythymidine Inhibitor

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

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

Protein crystallography data

The structure of Plasmodium Falciparum Thymidylate Kinase in Complex with A (Thio)Urea-Beta-Deoxythymidine Inhibitor, PDB code: 2yof 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) 94.95 / 1.82
Space group P 31 2 1
Cell size a, b, c (Å), α, β, γ (°) 109.639, 109.639, 121.892, 90.00, 90.00, 120.00
R / Rfree (%) 18.856 / 23.086

Other elements in 2yof:

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

Fluorine (F) 15 atoms

Chlorine Binding Sites:

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

Chlorine binding site 1 out of 5 in 2yof

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Chlorine binding site 1 out of 5 in the Plasmodium Falciparum Thymidylate Kinase in Complex with A (Thio)Urea-Beta-Deoxythymidine Inhibitor


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of Plasmodium Falciparum Thymidylate Kinase in Complex with A (Thio)Urea-Beta-Deoxythymidine Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl211

b:58.0
occ:0.50
 CL A:74W211 0.0 58.0 0.5
CL A:74W211 1.7 35.3 0.5
CAW A:74W211 1.7 57.5 0.5
FAG A:74W211 1.9 33.3 0.5
CAW A:74W211 2.0 31.9 0.5
CBE A:74W211 2.2 32.5 0.5
CAX A:74W211 2.3 32.0 0.5
FAH A:74W211 2.3 32.9 0.5
FAG A:74W211 2.7 59.5 0.5
CAX A:74W211 2.7 57.9 0.5
CAK A:74W211 2.7 56.9 0.5
NH2 A:ARG18 2.8 38.8 0.5
CBE A:74W211 3.0 59.0 0.5
FAH A:74W211 3.2 59.8 0.5
CAK A:74W211 3.2 31.3 0.5
CG A:GLU154 3.5 40.5 1.0
CAL A:74W211 3.5 29.9 0.5
FAF A:74W211 3.6 33.0 0.5
CD A:GLU154 3.8 41.8 0.5
OE2 A:GLU154 3.8 42.4 0.5
CZ A:ARG18 3.9 38.9 0.5
CAJ A:74W211 4.0 55.7 0.5
CAL A:74W211 4.0 56.1 0.5
CB A:GLU154 4.2 37.3 1.0
CAJ A:74W211 4.2 30.1 0.5
OE1 A:GLU150 4.3 50.2 1.0
FAF A:74W211 4.3 59.2 0.5
NH1 A:ARG18 4.3 38.9 0.5
CAV A:74W211 4.4 28.7 0.5
CD A:GLU150 4.4 48.4 1.0
OE1 A:GLU154 4.5 42.5 0.5
OE2 A:GLU150 4.5 49.7 1.0
CAV A:74W211 4.6 54.7 0.5
CB A:GLU151 4.7 35.8 1.0
CA A:GLU154 4.7 37.5 1.0
NE A:ARG18 4.9 39.6 0.5
N A:GLU151 4.9 37.7 1.0

Chlorine binding site 2 out of 5 in 2yof

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Chlorine binding site 2 out of 5 in the Plasmodium Falciparum Thymidylate Kinase in Complex with A (Thio)Urea-Beta-Deoxythymidine Inhibitor


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of Plasmodium Falciparum Thymidylate Kinase in Complex with A (Thio)Urea-Beta-Deoxythymidine Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl211

b:35.3
occ:0.50
 CL A:74W211 0.0 35.3 0.5
CL A:74W211 1.7 58.0 0.5
CAW A:74W211 1.8 31.9 0.5
CAW A:74W211 2.3 57.5 0.5
FAH A:74W211 2.6 32.9 0.5
CAX A:74W211 2.7 32.0 0.5
CAK A:74W211 2.8 31.3 0.5
CAK A:74W211 2.9 56.9 0.5
CBE A:74W211 3.1 32.5 0.5
CAX A:74W211 3.2 57.9 0.5
FAH A:74W211 3.2 59.8 0.5
CD A:GLU150 3.3 48.4 1.0
FAG A:74W211 3.4 33.3 0.5
N A:GLU151 3.5 37.7 1.0
CD A:GLU154 3.5 41.8 0.5
OE1 A:GLU150 3.5 50.2 1.0
CG A:GLU150 3.5 44.4 1.0
CB A:GLU151 3.6 35.8 1.0
OE2 A:GLU150 3.6 49.7 1.0
CBE A:74W211 3.6 59.0 0.5
CB A:GLU150 3.6 41.4 1.0
OE2 A:GLU154 3.7 42.4 0.5
FAG A:74W211 3.7 59.5 0.5
CG A:GLU154 3.8 40.5 1.0
OE1 A:GLU154 3.8 42.5 0.5
CG A:GLU151 4.0 35.2 1.0
CAL A:74W211 4.0 29.9 0.5
CAJ A:74W211 4.1 30.1 0.5
CAJ A:74W211 4.1 55.7 0.5
CA A:GLU151 4.1 35.9 1.0
C A:GLU150 4.1 39.8 1.0
NH2 A:ARG18 4.2 38.8 0.5
CB A:GLU154 4.2 37.3 1.0
CAL A:74W211 4.3 56.1 0.5
FAF A:74W211 4.3 33.0 0.5
CA A:GLU150 4.4 41.0 1.0
CAV A:74W211 4.6 28.7 0.5
CD A:GLU151 4.6 35.9 1.0
CAV A:74W211 4.7 54.7 0.5
OE1 A:GLU151 4.8 34.4 1.0
O A:GLU151 4.8 34.8 1.0
FAF A:74W211 4.9 59.2 0.5
O A:GLU150 4.9 40.2 1.0
C A:GLU151 4.9 35.0 1.0
N A:GLU150 5.0 41.4 1.0

Chlorine binding site 3 out of 5 in 2yof

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Chlorine binding site 3 out of 5 in the Plasmodium Falciparum Thymidylate Kinase in Complex with A (Thio)Urea-Beta-Deoxythymidine Inhibitor


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 3 of Plasmodium Falciparum Thymidylate Kinase in Complex with A (Thio)Urea-Beta-Deoxythymidine Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl211

b:47.1
occ:0.70
 CL B:74W211 0.0 47.1 0.7
CAW B:74W211 1.7 42.8 0.7
CAX B:74W211 2.7 41.5 0.7
CAK B:74W211 2.8 41.0 0.7
FAH B:74W211 2.8 41.5 0.7
FAG B:74W211 2.9 42.6 0.7
CBE B:74W211 2.9 42.1 0.7
O B:HOH2186 3.4 53.4 1.0
N B:GLU150 3.5 38.5 1.0
N B:GLU151 3.7 32.2 1.0
CB B:GLU151 3.7 29.9 0.5
CG B:GLU151 3.9 31.0 0.5
CB B:GLU151 3.9 31.0 0.5
CAL B:74W211 4.0 39.7 0.7
CB B:GLU154 4.0 31.6 1.0
OE1 B:GLU154 4.0 43.0 1.0
CAJ B:74W211 4.1 40.1 0.7
FAF B:74W211 4.3 42.2 0.7
CG B:GLU151 4.3 27.7 0.5
CA B:GLU151 4.3 30.6 0.5
C B:GLU150 4.3 35.3 1.0
CA B:GLU151 4.3 31.2 0.5
CA B:GLU150 4.4 37.7 1.0
CAV B:74W211 4.6 39.4 0.7
CD B:GLU151 4.7 25.3 0.5
OE1 B:GLU151 4.8 21.2 0.5
CD B:GLU154 4.8 40.9 1.0
O B:GLU151 4.8 30.3 1.0
CA B:GLU154 5.0 31.1 1.0

Chlorine binding site 4 out of 5 in 2yof

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Chlorine binding site 4 out of 5 in the Plasmodium Falciparum Thymidylate Kinase in Complex with A (Thio)Urea-Beta-Deoxythymidine Inhibitor


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 4 of Plasmodium Falciparum Thymidylate Kinase in Complex with A (Thio)Urea-Beta-Deoxythymidine Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Cl211

b:46.3
occ:0.50
 CL C:74W211 0.0 46.3 0.5
CAW C:74W211 1.7 42.8 0.5
CAX C:74W211 2.7 42.6 0.5
CAK C:74W211 2.7 41.3 0.5
FAH C:74W211 2.8 63.2 0.5
FAF C:74W211 2.8 43.9 0.5
FAH C:74W211 2.9 44.2 0.5
CBE C:74W211 3.0 43.5 0.5
CBE C:74W211 3.9 62.7 0.5
CAJ C:74W211 4.0 39.6 0.5
CAL C:74W211 4.0 40.0 0.5
CAX C:74W211 4.0 62.2 0.5
FAG C:74W211 4.3 43.6 0.5
CAW C:74W211 4.3 62.2 0.5
CAV C:74W211 4.5 37.7 0.5
CAL C:74W211 4.5 60.7 0.5
CL C:74W211 4.6 63.5 0.5
FAG C:74W211 4.6 63.0 0.5
FAF C:74W211 4.8 62.7 0.5

Chlorine binding site 5 out of 5 in 2yof

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


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 5 of Plasmodium Falciparum Thymidylate Kinase in Complex with A (Thio)Urea-Beta-Deoxythymidine Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Cl211

b:63.5
occ:0.50
 CL C:74W211 0.0 63.5 0.5
CAW C:74W211 1.7 62.2 0.5
FAG C:74W211 2.6 63.0 0.5
CAK C:74W211 2.7 61.5 0.5
CAX C:74W211 2.7 62.2 0.5
CBE C:74W211 3.1 62.7 0.5
FAH C:74W211 3.6 63.2 0.5
CB C:SER22 3.6 34.3 1.0
O C:HOH2017 3.8 47.8 1.0
CAJ C:74W211 4.0 60.4 0.5
CAL C:74W211 4.0 60.7 0.5
OG C:SER22 4.1 38.0 1.0
FAF C:74W211 4.1 43.9 0.5
FAF C:74W211 4.3 62.7 0.5
OD2 C:ASP98 4.5 31.3 1.0
CAW C:74W211 4.5 42.8 0.5
CAV C:74W211 4.5 59.4 0.5
CL C:74W211 4.6 46.3 0.5
CAX C:74W211 4.7 42.6 0.5
CAK C:74W211 4.8 41.3 0.5
CA C:SER22 5.0 34.0 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: Sat Jul 20 15:14:20 2024

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