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Fluorine in PDB 3dga: Wild-Type Plasmodium Falciparum Dihydrofolate Reductase-Thymidylate Synthase (Pfdhfr-Ts) Complexed with RJF01302, Nadph, and Dump

Enzymatic activity of Wild-Type Plasmodium Falciparum Dihydrofolate Reductase-Thymidylate Synthase (Pfdhfr-Ts) Complexed with RJF01302, Nadph, and Dump

All present enzymatic activity of Wild-Type Plasmodium Falciparum Dihydrofolate Reductase-Thymidylate Synthase (Pfdhfr-Ts) Complexed with RJF01302, Nadph, and Dump:
1.5.1.3; 2.1.1.45;

Protein crystallography data

The structure of Wild-Type Plasmodium Falciparum Dihydrofolate Reductase-Thymidylate Synthase (Pfdhfr-Ts) Complexed with RJF01302, Nadph, and Dump, PDB code: 3dga was solved by T.Dasgupta, P.Chitnumsub, C.Maneeruttanarungroj, S.Kamchonwongpaisan, S.Nichols, T.M.Lyons, J.Tirado-Rives, W.L.Jorgensen, Y.Yuthavong, K.S.Anderson, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 29.18 / 2.70
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 57.377, 156.015, 164.567, 90.00, 90.00, 90.00
R / Rfree (%) 20.5 / 25.6

Other elements in 3dga:

The structure of Wild-Type Plasmodium Falciparum Dihydrofolate Reductase-Thymidylate Synthase (Pfdhfr-Ts) Complexed with RJF01302, Nadph, and Dump also contains other interesting chemical elements:

Chlorine (Cl) 2 atoms

Fluorine Binding Sites:

The binding sites of Fluorine atom in the Wild-Type Plasmodium Falciparum Dihydrofolate Reductase-Thymidylate Synthase (Pfdhfr-Ts) Complexed with RJF01302, Nadph, and Dump (pdb code 3dga). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 6 binding sites of Fluorine where determined in the Wild-Type Plasmodium Falciparum Dihydrofolate Reductase-Thymidylate Synthase (Pfdhfr-Ts) Complexed with RJF01302, Nadph, and Dump, PDB code: 3dga:
Jump to Fluorine binding site number: 1; 2; 3; 4; 5; 6;

Fluorine binding site 1 out of 6 in 3dga

Go back to Fluorine Binding Sites List in 3dga
Fluorine binding site 1 out of 6 in the Wild-Type Plasmodium Falciparum Dihydrofolate Reductase-Thymidylate Synthase (Pfdhfr-Ts) Complexed with RJF01302, Nadph, and Dump


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of Wild-Type Plasmodium Falciparum Dihydrofolate Reductase-Thymidylate Synthase (Pfdhfr-Ts) Complexed with RJF01302, Nadph, and Dump within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F609

b:87.1
occ:1.00
 F9 A:RJ1609 0.0 87.1 1.0
C8 A:RJ1609 1.4 84.4 1.0
F11 A:RJ1609 2.2 85.2 1.0
F10 A:RJ1609 2.3 84.1 1.0
C1 A:RJ1609 2.4 82.3 1.0
SD A:MET55 2.7 54.5 1.0
C6 A:RJ1609 2.8 80.2 1.0
CE A:MET55 3.2 52.9 1.0
C2 A:RJ1609 3.7 81.3 1.0
C5 A:RJ1609 4.2 79.5 1.0
CG A:MET55 4.3 46.9 1.0
C3 A:RJ1609 4.8 81.5 1.0

Fluorine binding site 2 out of 6 in 3dga

Go back to Fluorine Binding Sites List in 3dga
Fluorine binding site 2 out of 6 in the Wild-Type Plasmodium Falciparum Dihydrofolate Reductase-Thymidylate Synthase (Pfdhfr-Ts) Complexed with RJF01302, Nadph, and Dump


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of Wild-Type Plasmodium Falciparum Dihydrofolate Reductase-Thymidylate Synthase (Pfdhfr-Ts) Complexed with RJF01302, Nadph, and Dump within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F609

b:84.1
occ:1.00
 F10 A:RJ1609 0.0 84.1 1.0
C8 A:RJ1609 1.4 84.4 1.0
F9 A:RJ1609 2.3 87.1 1.0
F11 A:RJ1609 2.3 85.2 1.0
C1 A:RJ1609 2.4 82.3 1.0
C2 A:RJ1609 3.1 81.3 1.0
C6 A:RJ1609 3.5 80.2 1.0
SD A:MET55 4.0 54.5 1.0
CD2 A:LEU119 4.2 32.1 1.0
C3 A:RJ1609 4.3 81.5 1.0
CD2 A:PHE116 4.4 57.1 1.0
C5 A:RJ1609 4.6 79.5 1.0
CE2 A:PHE58 4.7 25.3 1.0
CD2 A:PHE58 4.8 24.3 1.0
CE2 A:PHE116 4.9 57.5 1.0
CD1 A:ILE112 4.9 44.9 1.0
CG1 A:ILE112 5.0 43.3 1.0
CE A:MET55 5.0 52.9 1.0
C4 A:RJ1609 5.0 80.6 1.0
CG A:PHE116 5.0 55.7 1.0

Fluorine binding site 3 out of 6 in 3dga

Go back to Fluorine Binding Sites List in 3dga
Fluorine binding site 3 out of 6 in the Wild-Type Plasmodium Falciparum Dihydrofolate Reductase-Thymidylate Synthase (Pfdhfr-Ts) Complexed with RJF01302, Nadph, and Dump


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of Wild-Type Plasmodium Falciparum Dihydrofolate Reductase-Thymidylate Synthase (Pfdhfr-Ts) Complexed with RJF01302, Nadph, and Dump within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F609

b:85.2
occ:1.00
 F11 A:RJ1609 0.0 85.2 1.0
C8 A:RJ1609 1.4 84.4 1.0
F9 A:RJ1609 2.2 87.1 1.0
F10 A:RJ1609 2.3 84.1 1.0
C1 A:RJ1609 2.4 82.3 1.0
C2 A:RJ1609 2.9 81.3 1.0
C6 A:RJ1609 3.6 80.2 1.0
CG1 A:ILE112 3.8 43.3 1.0
C3 A:RJ1609 4.2 81.5 1.0
CG2 A:ILE112 4.3 43.3 1.0
CD1 A:ILE112 4.4 44.9 1.0
CD2 A:PHE116 4.5 57.1 1.0
CB A:ILE112 4.5 44.4 1.0
CD A:PRO113 4.6 48.1 1.0
CA A:ILE112 4.6 44.8 1.0
C5 A:RJ1609 4.7 79.5 1.0
SD A:MET55 4.9 54.5 1.0
C4 A:RJ1609 4.9 80.6 1.0
CE2 A:PHE116 5.0 57.5 1.0

Fluorine binding site 4 out of 6 in 3dga

Go back to Fluorine Binding Sites List in 3dga
Fluorine binding site 4 out of 6 in the Wild-Type Plasmodium Falciparum Dihydrofolate Reductase-Thymidylate Synthase (Pfdhfr-Ts) Complexed with RJF01302, Nadph, and Dump


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 4 of Wild-Type Plasmodium Falciparum Dihydrofolate Reductase-Thymidylate Synthase (Pfdhfr-Ts) Complexed with RJF01302, Nadph, and Dump within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F609

b:90.0
occ:1.00
 F9 B:RJ1609 0.0 90.0 1.0
C8 B:RJ1609 1.4 90.0 1.0
F11 B:RJ1609 2.2 90.0 1.0
F10 B:RJ1609 2.2 90.0 1.0
C1 B:RJ1609 2.4 90.0 1.0
SD B:MET55 2.8 66.6 1.0
C6 B:RJ1609 2.8 89.7 1.0
CE B:MET55 3.0 66.2 1.0
C2 B:RJ1609 3.7 90.0 1.0
C5 B:RJ1609 4.2 89.8 1.0
CG B:MET55 4.5 60.8 1.0
C3 B:RJ1609 4.8 90.0 1.0

Fluorine binding site 5 out of 6 in 3dga

Go back to Fluorine Binding Sites List in 3dga
Fluorine binding site 5 out of 6 in the Wild-Type Plasmodium Falciparum Dihydrofolate Reductase-Thymidylate Synthase (Pfdhfr-Ts) Complexed with RJF01302, Nadph, and Dump


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 5 of Wild-Type Plasmodium Falciparum Dihydrofolate Reductase-Thymidylate Synthase (Pfdhfr-Ts) Complexed with RJF01302, Nadph, and Dump within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F609

b:90.0
occ:1.00
 F10 B:RJ1609 0.0 90.0 1.0
C8 B:RJ1609 1.4 90.0 1.0
F9 B:RJ1609 2.2 90.0 1.0
F11 B:RJ1609 2.3 90.0 1.0
C1 B:RJ1609 2.4 90.0 1.0
C2 B:RJ1609 3.1 90.0 1.0
C6 B:RJ1609 3.5 89.7 1.0
SD B:MET55 4.0 66.6 1.0
CD2 B:LEU119 4.1 74.0 1.0
C3 B:RJ1609 4.3 90.0 1.0
CE2 B:PHE58 4.6 58.6 1.0
CD2 B:PHE58 4.6 57.9 1.0
C5 B:RJ1609 4.6 89.8 1.0
CE B:MET55 5.0 66.2 1.0
C4 B:RJ1609 5.0 90.0 1.0

Fluorine binding site 6 out of 6 in 3dga

Go back to Fluorine Binding Sites List in 3dga
Fluorine binding site 6 out of 6 in the Wild-Type Plasmodium Falciparum Dihydrofolate Reductase-Thymidylate Synthase (Pfdhfr-Ts) Complexed with RJF01302, Nadph, and Dump


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 6 of Wild-Type Plasmodium Falciparum Dihydrofolate Reductase-Thymidylate Synthase (Pfdhfr-Ts) Complexed with RJF01302, Nadph, and Dump within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F609

b:90.0
occ:1.00
 F11 B:RJ1609 0.0 90.0 1.0
C8 B:RJ1609 1.4 90.0 1.0
F9 B:RJ1609 2.2 90.0 1.0
F10 B:RJ1609 2.3 90.0 1.0
C1 B:RJ1609 2.4 90.0 1.0
C2 B:RJ1609 2.9 90.0 1.0
C6 B:RJ1609 3.6 89.7 1.0
C3 B:RJ1609 4.2 90.0 1.0
CD B:PRO113 4.2 84.0 1.0
CG2 B:ILE112 4.5 79.8 1.0
C5 B:RJ1609 4.7 89.8 1.0
CG1 B:ILE112 4.7 79.5 1.0
CG B:PRO113 4.8 83.7 1.0
SD B:MET55 4.8 66.6 1.0
C4 B:RJ1609 4.9 90.0 1.0
CA B:ILE112 5.0 80.2 1.0
CB B:ILE112 5.0 80.0 1.0

Reference:

T.Dasgupta, P.Chitnumsub, S.Kamchonwongpaisan, C.Maneeruttanarungroj, S.E.Nichols, T.M.Lyons, J.Tirado-Rives, W.L.Jorgensen, Y.Yuthavong, K.S.Anderson. Exploiting Structural Analysis, in Silico Screening, and Serendipity to Identify Novel Inhibitors of Drug-Resistant Falciparum Malaria. Acs Chem.Biol. V. 4 29 2009.
ISSN: ISSN 1554-8929
PubMed: 19146480
DOI: 10.1021/CB8002804
Page generated: Sun Dec 13 11:44:47 2020

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