Fluorine in PDB 6gjg: Plasmodium Falciparum Dihydroorotate Dehydrogenase Dhodh in Complex with 3,6-Dimethyl-N-(4-(Trifluoromethyl)Phenyl)-(1,2)Oxazolo(5,4-D) Pyrimidin-4-Amine

Enzymatic activity of Plasmodium Falciparum Dihydroorotate Dehydrogenase Dhodh in Complex with 3,6-Dimethyl-N-(4-(Trifluoromethyl)Phenyl)-(1,2)Oxazolo(5,4-D) Pyrimidin-4-Amine

All present enzymatic activity of Plasmodium Falciparum Dihydroorotate Dehydrogenase Dhodh in Complex with 3,6-Dimethyl-N-(4-(Trifluoromethyl)Phenyl)-(1,2)Oxazolo(5,4-D) Pyrimidin-4-Amine:
1.3.5.2;

Protein crystallography data

The structure of Plasmodium Falciparum Dihydroorotate Dehydrogenase Dhodh in Complex with 3,6-Dimethyl-N-(4-(Trifluoromethyl)Phenyl)-(1,2)Oxazolo(5,4-D) Pyrimidin-4-Amine, PDB code: 6gjg was solved by P.Rowland, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 21.80 / 1.99
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 58.730, 162.950, 64.740, 90.00, 112.90, 90.00
R / Rfree (%) 16.3 / 20.6

Fluorine Binding Sites:

The binding sites of Fluorine atom in the Plasmodium Falciparum Dihydroorotate Dehydrogenase Dhodh in Complex with 3,6-Dimethyl-N-(4-(Trifluoromethyl)Phenyl)-(1,2)Oxazolo(5,4-D) Pyrimidin-4-Amine (pdb code 6gjg). 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 Dihydroorotate Dehydrogenase Dhodh in Complex with 3,6-Dimethyl-N-(4-(Trifluoromethyl)Phenyl)-(1,2)Oxazolo(5,4-D) Pyrimidin-4-Amine, PDB code: 6gjg:
Jump to Fluorine binding site number: 1; 2; 3; 4; 5; 6;

Fluorine binding site 1 out of 6 in 6gjg

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Fluorine binding site 1 out of 6 in the Plasmodium Falciparum Dihydroorotate Dehydrogenase Dhodh in Complex with 3,6-Dimethyl-N-(4-(Trifluoromethyl)Phenyl)-(1,2)Oxazolo(5,4-D) Pyrimidin-4-Amine


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of Plasmodium Falciparum Dihydroorotate Dehydrogenase Dhodh in Complex with 3,6-Dimethyl-N-(4-(Trifluoromethyl)Phenyl)-(1,2)Oxazolo(5,4-D) Pyrimidin-4-Amine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F603

b:66.5
occ:1.00
 F2 A:F1T603 0.0 66.5 1.0
C12 A:F1T603 1.3 65.7 1.0
F A:F1T603 2.1 65.0 1.0
F1 A:F1T603 2.1 69.0 1.0
C9 A:F1T603 2.4 60.6 1.0
C8 A:F1T603 2.7 55.7 1.0
C10 A:F1T603 3.6 58.7 1.0
CD1 A:LEU240 3.8 41.5 1.0
C7 A:F1T603 4.1 51.9 1.0
CD1 A:LEU197 4.1 67.9 1.0
CE2 A:PHE227 4.2 35.8 1.0
CZ A:PHE227 4.6 34.8 1.0
CB A:PHE188 4.6 52.4 1.0
CG1 A:ILE237 4.7 31.5 1.0
CG A:MET536 4.8 65.9 1.0
C11 A:F1T603 4.8 55.4 1.0
CD2 A:LEU531 4.8 46.5 1.0
O A:PHE188 4.9 49.4 1.0
C6 A:F1T603 5.0 51.1 1.0

Fluorine binding site 2 out of 6 in 6gjg

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Fluorine binding site 2 out of 6 in the Plasmodium Falciparum Dihydroorotate Dehydrogenase Dhodh in Complex with 3,6-Dimethyl-N-(4-(Trifluoromethyl)Phenyl)-(1,2)Oxazolo(5,4-D) Pyrimidin-4-Amine


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of Plasmodium Falciparum Dihydroorotate Dehydrogenase Dhodh in Complex with 3,6-Dimethyl-N-(4-(Trifluoromethyl)Phenyl)-(1,2)Oxazolo(5,4-D) Pyrimidin-4-Amine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F603

b:65.0
occ:1.00
 F A:F1T603 0.0 65.0 1.0
C12 A:F1T603 1.3 65.7 1.0
F2 A:F1T603 2.1 66.5 1.0
F1 A:F1T603 2.2 69.0 1.0
C9 A:F1T603 2.4 60.6 1.0
C10 A:F1T603 2.9 58.7 1.0
CD2 A:LEU531 3.4 46.5 1.0
C8 A:F1T603 3.5 55.7 1.0
CD1 A:LEU240 3.7 41.5 1.0
CG A:MET536 3.8 65.9 1.0
N A:MET536 4.1 56.5 1.0
CA A:MET536 4.1 57.3 1.0
C A:GLY535 4.2 55.9 1.0
C11 A:F1T603 4.3 55.4 1.0
CB A:LEU531 4.3 34.7 1.0
O A:GLY535 4.3 54.1 1.0
CG A:LEU531 4.4 39.8 1.0
O A:LEU531 4.5 42.4 1.0
CB A:MET536 4.6 63.0 1.0
C7 A:F1T603 4.7 51.9 1.0
CZ A:PHE227 4.8 34.8 1.0
CA A:GLY535 4.9 48.8 1.0
CE2 A:PHE227 5.0 35.8 1.0
CA A:LEU531 5.0 36.2 1.0
CE A:MET536 5.0 70.2 1.0
CG A:LEU240 5.0 44.6 1.0
C6 A:F1T603 5.0 51.1 1.0

Fluorine binding site 3 out of 6 in 6gjg

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Fluorine binding site 3 out of 6 in the Plasmodium Falciparum Dihydroorotate Dehydrogenase Dhodh in Complex with 3,6-Dimethyl-N-(4-(Trifluoromethyl)Phenyl)-(1,2)Oxazolo(5,4-D) Pyrimidin-4-Amine


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of Plasmodium Falciparum Dihydroorotate Dehydrogenase Dhodh in Complex with 3,6-Dimethyl-N-(4-(Trifluoromethyl)Phenyl)-(1,2)Oxazolo(5,4-D) Pyrimidin-4-Amine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F603

b:69.0
occ:1.00
 F1 A:F1T603 0.0 69.0 1.0
C12 A:F1T603 1.3 65.7 1.0
F2 A:F1T603 2.1 66.5 1.0
F A:F1T603 2.2 65.0 1.0
C9 A:F1T603 2.4 60.6 1.0
C10 A:F1T603 3.1 58.7 1.0
CE A:MET536 3.3 70.2 1.0
CG A:MET536 3.3 65.9 1.0
C8 A:F1T603 3.4 55.7 1.0
SD A:MET536 4.1 75.5 1.0
CG A:PHE188 4.1 57.6 1.0
CB A:PHE188 4.2 52.4 1.0
CD2 A:PHE188 4.3 59.8 1.0
C11 A:F1T603 4.3 55.4 1.0
CD1 A:LEU197 4.4 67.9 1.0
C7 A:F1T603 4.5 51.9 1.0
CD2 A:LEU197 4.6 75.2 1.0
CD1 A:PHE188 4.6 65.3 1.0
CB A:MET536 4.6 63.0 1.0
N A:MET536 4.7 56.5 1.0
CD1 A:LEU240 4.7 41.5 1.0
CA A:MET536 4.8 57.3 1.0
CE2 A:PHE188 4.8 65.8 1.0
C6 A:F1T603 4.9 51.1 1.0

Fluorine binding site 4 out of 6 in 6gjg

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Fluorine binding site 4 out of 6 in the Plasmodium Falciparum Dihydroorotate Dehydrogenase Dhodh in Complex with 3,6-Dimethyl-N-(4-(Trifluoromethyl)Phenyl)-(1,2)Oxazolo(5,4-D) Pyrimidin-4-Amine


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 4 of Plasmodium Falciparum Dihydroorotate Dehydrogenase Dhodh in Complex with 3,6-Dimethyl-N-(4-(Trifluoromethyl)Phenyl)-(1,2)Oxazolo(5,4-D) Pyrimidin-4-Amine within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F603

b:77.1
occ:1.00
 F2 B:F1T603 0.0 77.1 1.0
C12 B:F1T603 1.3 78.8 1.0
F B:F1T603 2.1 80.7 1.0
F1 B:F1T603 2.1 83.1 1.0
C9 B:F1T603 2.4 73.7 1.0
C8 B:F1T603 2.8 68.6 1.0
C10 B:F1T603 3.6 73.7 1.0
CD1 B:LEU240 3.6 52.2 1.0
CE2 B:PHE227 4.0 46.1 1.0
C7 B:F1T603 4.2 64.6 1.0
CD2 B:LEU531 4.2 54.6 1.0
CZ B:PHE227 4.3 44.7 1.0
CD1 B:LEU197 4.5 79.1 1.0
CG1 B:ILE237 4.7 45.1 1.0
C11 B:F1T603 4.7 70.8 1.0
CG B:MET536 4.8 75.0 1.0
CB B:PHE188 5.0 70.6 1.0
C6 B:F1T603 5.0 65.1 1.0

Fluorine binding site 5 out of 6 in 6gjg

Go back to Fluorine Binding Sites List in 6gjg
Fluorine binding site 5 out of 6 in the Plasmodium Falciparum Dihydroorotate Dehydrogenase Dhodh in Complex with 3,6-Dimethyl-N-(4-(Trifluoromethyl)Phenyl)-(1,2)Oxazolo(5,4-D) Pyrimidin-4-Amine


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 5 of Plasmodium Falciparum Dihydroorotate Dehydrogenase Dhodh in Complex with 3,6-Dimethyl-N-(4-(Trifluoromethyl)Phenyl)-(1,2)Oxazolo(5,4-D) Pyrimidin-4-Amine within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F603

b:80.7
occ:1.00
 F B:F1T603 0.0 80.7 1.0
C12 B:F1T603 1.3 78.8 1.0
F2 B:F1T603 2.1 77.1 1.0
F1 B:F1T603 2.1 83.1 1.0
C9 B:F1T603 2.4 73.7 1.0
C10 B:F1T603 2.8 73.7 1.0
CD2 B:LEU531 3.3 54.6 1.0
CG B:MET536 3.6 75.0 1.0
C8 B:F1T603 3.6 68.6 1.0
N B:MET536 3.9 67.2 1.0
C B:GLY535 3.9 67.7 1.0
CA B:MET536 4.0 67.3 1.0
O B:GLY535 4.0 65.1 1.0
CD1 B:LEU240 4.0 52.2 1.0
C11 B:F1T603 4.2 70.8 1.0
O B:LEU531 4.3 59.2 1.0
CB B:LEU531 4.3 47.3 1.0
CB B:MET536 4.4 72.8 1.0
CG B:LEU531 4.4 50.7 1.0
CE B:MET536 4.6 79.2 1.0
CA B:GLY535 4.6 64.3 1.0
C7 B:F1T603 4.7 64.6 1.0
CZ B:PHE227 4.9 44.7 1.0
SD B:MET536 4.9 84.1 1.0
CA B:LEU531 5.0 49.9 1.0
C6 B:F1T603 5.0 65.1 1.0

Fluorine binding site 6 out of 6 in 6gjg

Go back to Fluorine Binding Sites List in 6gjg
Fluorine binding site 6 out of 6 in the Plasmodium Falciparum Dihydroorotate Dehydrogenase Dhodh in Complex with 3,6-Dimethyl-N-(4-(Trifluoromethyl)Phenyl)-(1,2)Oxazolo(5,4-D) Pyrimidin-4-Amine


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 6 of Plasmodium Falciparum Dihydroorotate Dehydrogenase Dhodh in Complex with 3,6-Dimethyl-N-(4-(Trifluoromethyl)Phenyl)-(1,2)Oxazolo(5,4-D) Pyrimidin-4-Amine within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F603

b:83.1
occ:1.00
 F1 B:F1T603 0.0 83.1 1.0
C12 B:F1T603 1.3 78.8 1.0
F B:F1T603 2.1 80.7 1.0
F2 B:F1T603 2.1 77.1 1.0
C9 B:F1T603 2.4 73.7 1.0
C10 B:F1T603 3.2 73.7 1.0
C8 B:F1T603 3.2 68.6 1.0
CE B:MET536 3.3 79.2 1.0
CG B:MET536 3.5 75.0 1.0
CB B:PHE188 3.9 70.6 1.0
CG B:PHE188 4.0 76.6 1.0
SD B:MET536 4.2 84.1 1.0
CD1 B:LEU197 4.2 79.1 1.0
CD1 B:PHE188 4.2 84.5 1.0
C11 B:F1T603 4.4 70.8 1.0
C7 B:F1T603 4.4 64.6 1.0
CD2 B:LEU197 4.5 86.6 1.0
CD2 B:PHE188 4.5 79.0 1.0
CD1 B:LEU240 4.7 52.2 1.0
CB B:MET536 4.9 72.8 1.0
C6 B:F1T603 4.9 65.1 1.0
CE1 B:PHE188 4.9 89.0 1.0
O B:PHE188 5.0 65.1 1.0

Reference:

S.Kokkonda, F.El Mazouni, K.L.White, J.White, D.M.Shackleford, M.J.Lafuente-Monasterio, P.Rowland, K.Manjalanagara, J.T.Joseph, A.Garcia-Perez, J.Fernandez, F.J.Gamo, D.Waterson, J.N.Burrows, M.J.Palmer, S.A.Charman, P.K.Rathod, M.A.Phillips. Isoxazolopyrimidine-Based Inhibitors Ofplasmodium Falciparumdihydroorotate Dehydrogenase with Antimalarial Activity. Acs Omega V. 3 9227 2018.
ISSN: ESSN 2470-1343
PubMed: 30197997
DOI: 10.1021/ACSOMEGA.8B01573
Page generated: Sun Dec 13 12:51:27 2020

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