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Fluorine in PDB 4ori: Rat Dihydroorotate Dehydrogenase Bound with DSM338 (N-[3,5-Difluoro-4- (Trifluoromethyl)Phenyl]-5-Methyl-2-(Trifluoromethyl)[1,2, 4]Triazolo[1,5-A]Pyrimidin-7-Amine)

Enzymatic activity of Rat Dihydroorotate Dehydrogenase Bound with DSM338 (N-[3,5-Difluoro-4- (Trifluoromethyl)Phenyl]-5-Methyl-2-(Trifluoromethyl)[1,2, 4]Triazolo[1,5-A]Pyrimidin-7-Amine)

All present enzymatic activity of Rat Dihydroorotate Dehydrogenase Bound with DSM338 (N-[3,5-Difluoro-4- (Trifluoromethyl)Phenyl]-5-Methyl-2-(Trifluoromethyl)[1,2, 4]Triazolo[1,5-A]Pyrimidin-7-Amine):
1.3.5.2;

Protein crystallography data

The structure of Rat Dihydroorotate Dehydrogenase Bound with DSM338 (N-[3,5-Difluoro-4- (Trifluoromethyl)Phenyl]-5-Methyl-2-(Trifluoromethyl)[1,2, 4]Triazolo[1,5-A]Pyrimidin-7-Amine), PDB code: 4ori was solved by X.Deng, M.A.Phillips, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 20.00 / 1.50
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 124.365, 43.845, 63.305, 90.00, 99.96, 90.00
R / Rfree (%) 18 / 23.4

Fluorine Binding Sites:

The binding sites of Fluorine atom in the Rat Dihydroorotate Dehydrogenase Bound with DSM338 (N-[3,5-Difluoro-4- (Trifluoromethyl)Phenyl]-5-Methyl-2-(Trifluoromethyl)[1,2, 4]Triazolo[1,5-A]Pyrimidin-7-Amine) (pdb code 4ori). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 8 binding sites of Fluorine where determined in the Rat Dihydroorotate Dehydrogenase Bound with DSM338 (N-[3,5-Difluoro-4- (Trifluoromethyl)Phenyl]-5-Methyl-2-(Trifluoromethyl)[1,2, 4]Triazolo[1,5-A]Pyrimidin-7-Amine), PDB code: 4ori:
Jump to Fluorine binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Fluorine binding site 1 out of 8 in 4ori

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Fluorine binding site 1 out of 8 in the Rat Dihydroorotate Dehydrogenase Bound with DSM338 (N-[3,5-Difluoro-4- (Trifluoromethyl)Phenyl]-5-Methyl-2-(Trifluoromethyl)[1,2, 4]Triazolo[1,5-A]Pyrimidin-7-Amine)


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of Rat Dihydroorotate Dehydrogenase Bound with DSM338 (N-[3,5-Difluoro-4- (Trifluoromethyl)Phenyl]-5-Methyl-2-(Trifluoromethyl)[1,2, 4]Triazolo[1,5-A]Pyrimidin-7-Amine) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F502

b:34.4
occ:1.00
 F8 A:2V6502 0.0 34.4 1.0
C5 A:2V6502 1.3 27.5 1.0
C6 A:2V6502 2.3 26.3 1.0
C4 A:2V6502 2.4 29.4 1.0
F1 A:2V6502 2.6 38.8 1.0
C7 A:2V6502 3.0 38.8 1.0
C1 A:2V6502 3.5 26.8 1.0
C3 A:2V6502 3.6 32.2 1.0
O A:LEU359 3.9 23.3 1.0
F2 A:2V6502 3.9 47.8 1.0
CD A:PRO364 4.0 30.8 1.0
F3 A:2V6502 4.0 33.6 1.0
C2 A:2V6502 4.1 29.4 1.0
CA A:GLY363 4.2 25.1 1.0
CG A:PRO364 4.2 37.1 1.0
N A:PRO364 4.3 27.4 1.0
CB A:LEU359 4.4 23.4 1.0
CE A:MET43 4.5 30.4 1.0
C A:GLY363 4.5 23.8 1.0
C A:LEU359 4.5 23.5 1.0
N1 A:2V6502 4.6 28.3 1.0
CD2 A:LEU359 4.6 32.1 1.0
F7 A:2V6502 4.7 35.8 1.0
CB A:ALA59 4.7 27.2 1.0
CA A:LEU359 4.9 21.2 1.0

Fluorine binding site 2 out of 8 in 4ori

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Fluorine binding site 2 out of 8 in the Rat Dihydroorotate Dehydrogenase Bound with DSM338 (N-[3,5-Difluoro-4- (Trifluoromethyl)Phenyl]-5-Methyl-2-(Trifluoromethyl)[1,2, 4]Triazolo[1,5-A]Pyrimidin-7-Amine)


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of Rat Dihydroorotate Dehydrogenase Bound with DSM338 (N-[3,5-Difluoro-4- (Trifluoromethyl)Phenyl]-5-Methyl-2-(Trifluoromethyl)[1,2, 4]Triazolo[1,5-A]Pyrimidin-7-Amine) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F502

b:33.6
occ:1.00
 F3 A:2V6502 0.0 33.6 1.0
C7 A:2V6502 1.3 38.8 1.0
F2 A:2V6502 2.1 47.8 1.0
F1 A:2V6502 2.2 38.8 1.0
C4 A:2V6502 2.4 29.4 1.0
F7 A:2V6502 2.7 35.8 1.0
C3 A:2V6502 2.9 32.2 1.0
C5 A:2V6502 3.5 27.5 1.0
F8 A:2V6502 4.0 34.4 1.0
CG1 A:VAL62 4.0 40.0 1.0
CD2 A:LEU68 4.1 48.2 1.0
CA A:ALA59 4.1 25.7 1.0
C2 A:2V6502 4.2 29.4 1.0
CD1 A:LEU68 4.3 42.9 1.0
CB A:ALA59 4.3 27.2 1.0
CB A:VAL62 4.4 29.2 1.0
CG A:LEU68 4.6 40.0 1.0
O A:ALA59 4.7 27.4 1.0
C6 A:2V6502 4.7 26.3 1.0
C A:ALA59 4.9 24.4 1.0
N A:ALA59 4.9 25.1 1.0
C1 A:2V6502 5.0 26.8 1.0

Fluorine binding site 3 out of 8 in 4ori

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Fluorine binding site 3 out of 8 in the Rat Dihydroorotate Dehydrogenase Bound with DSM338 (N-[3,5-Difluoro-4- (Trifluoromethyl)Phenyl]-5-Methyl-2-(Trifluoromethyl)[1,2, 4]Triazolo[1,5-A]Pyrimidin-7-Amine)


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of Rat Dihydroorotate Dehydrogenase Bound with DSM338 (N-[3,5-Difluoro-4- (Trifluoromethyl)Phenyl]-5-Methyl-2-(Trifluoromethyl)[1,2, 4]Triazolo[1,5-A]Pyrimidin-7-Amine) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F502

b:47.8
occ:1.00
 F2 A:2V6502 0.0 47.8 1.0
C7 A:2V6502 1.3 38.8 1.0
F3 A:2V6502 2.1 33.6 1.0
F1 A:2V6502 2.1 38.8 1.0
C4 A:2V6502 2.3 29.4 1.0
F7 A:2V6502 2.7 35.8 1.0
C3 A:2V6502 2.9 32.2 1.0
C5 A:2V6502 3.5 27.5 1.0
CD2 A:LEU42 3.7 50.6 1.0
F8 A:2V6502 3.9 34.4 1.0
C2 A:2V6502 4.2 29.4 1.0
SD A:MET43 4.2 35.8 1.0
CE2 A:TYR38 4.3 43.3 1.0
CD1 A:LEU46 4.3 40.5 1.0
CE A:MET43 4.6 30.4 1.0
CD2 A:LEU68 4.6 48.2 1.0
CD A:PRO364 4.6 30.8 1.0
C6 A:2V6502 4.7 26.3 1.0
CD2 A:TYR38 4.7 39.4 1.0
C1 A:2V6502 4.9 26.8 1.0
CG A:LEU42 4.9 46.9 1.0

Fluorine binding site 4 out of 8 in 4ori

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Fluorine binding site 4 out of 8 in the Rat Dihydroorotate Dehydrogenase Bound with DSM338 (N-[3,5-Difluoro-4- (Trifluoromethyl)Phenyl]-5-Methyl-2-(Trifluoromethyl)[1,2, 4]Triazolo[1,5-A]Pyrimidin-7-Amine)


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 4 of Rat Dihydroorotate Dehydrogenase Bound with DSM338 (N-[3,5-Difluoro-4- (Trifluoromethyl)Phenyl]-5-Methyl-2-(Trifluoromethyl)[1,2, 4]Triazolo[1,5-A]Pyrimidin-7-Amine) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F502

b:38.8
occ:1.00
 F1 A:2V6502 0.0 38.8 1.0
C7 A:2V6502 1.3 38.8 1.0
F2 A:2V6502 2.1 47.8 1.0
F3 A:2V6502 2.2 33.6 1.0
C4 A:2V6502 2.4 29.4 1.0
F8 A:2V6502 2.6 34.4 1.0
C5 A:2V6502 2.8 27.5 1.0
CD A:PRO364 3.3 30.8 1.0
CG A:PRO364 3.4 37.1 1.0
C3 A:2V6502 3.6 32.2 1.0
CD1 A:LEU68 3.9 42.9 1.0
CD2 A:LEU68 3.9 48.2 1.0
F7 A:2V6502 4.0 35.8 1.0
C6 A:2V6502 4.2 26.3 1.0
N A:PRO364 4.5 27.4 1.0
CE2 A:TYR38 4.5 43.3 1.0
CG A:LEU68 4.6 40.0 1.0
C2 A:2V6502 4.8 29.4 1.0
CB A:PRO364 4.8 34.8 1.0
CD2 A:TYR38 4.9 39.4 1.0
CA A:GLY363 5.0 25.1 1.0
C1 A:2V6502 5.0 26.8 1.0

Fluorine binding site 5 out of 8 in 4ori

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Fluorine binding site 5 out of 8 in the Rat Dihydroorotate Dehydrogenase Bound with DSM338 (N-[3,5-Difluoro-4- (Trifluoromethyl)Phenyl]-5-Methyl-2-(Trifluoromethyl)[1,2, 4]Triazolo[1,5-A]Pyrimidin-7-Amine)


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 5 of Rat Dihydroorotate Dehydrogenase Bound with DSM338 (N-[3,5-Difluoro-4- (Trifluoromethyl)Phenyl]-5-Methyl-2-(Trifluoromethyl)[1,2, 4]Triazolo[1,5-A]Pyrimidin-7-Amine) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F502

b:35.8
occ:1.00
 F7 A:2V6502 0.0 35.8 1.0
C3 A:2V6502 1.3 32.2 1.0
C4 A:2V6502 2.3 29.4 1.0
C2 A:2V6502 2.4 29.4 1.0
C7 A:2V6502 2.7 38.8 1.0
F3 A:2V6502 2.7 33.6 1.0
F2 A:2V6502 2.7 47.8 1.0
C5 A:2V6502 3.6 27.5 1.0
C1 A:2V6502 3.6 26.8 1.0
CD1 A:LEU46 3.7 40.5 1.0
F1 A:2V6502 4.0 38.8 1.0
CB A:ALA59 4.1 27.2 1.0
C6 A:2V6502 4.1 26.3 1.0
CA A:ALA59 4.2 25.7 1.0
N A:ALA59 4.4 25.1 1.0
O A:ALA55 4.5 27.4 1.0
CD2 A:LEU58 4.7 33.1 1.0
F8 A:2V6502 4.7 34.4 1.0
CG A:LEU58 4.7 32.5 1.0
N1 A:2V6502 4.8 28.3 1.0
CE A:MET43 4.8 30.4 1.0
C A:LEU58 5.0 28.0 1.0
C9 A:2V6502 5.0 28.6 1.0

Fluorine binding site 6 out of 8 in 4ori

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Fluorine binding site 6 out of 8 in the Rat Dihydroorotate Dehydrogenase Bound with DSM338 (N-[3,5-Difluoro-4- (Trifluoromethyl)Phenyl]-5-Methyl-2-(Trifluoromethyl)[1,2, 4]Triazolo[1,5-A]Pyrimidin-7-Amine)


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 6 of Rat Dihydroorotate Dehydrogenase Bound with DSM338 (N-[3,5-Difluoro-4- (Trifluoromethyl)Phenyl]-5-Methyl-2-(Trifluoromethyl)[1,2, 4]Triazolo[1,5-A]Pyrimidin-7-Amine) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F502

b:33.8
occ:1.00
 F6 A:2V6502 0.0 33.8 1.0
C14 A:2V6502 1.3 29.0 1.0
F5 A:2V6502 2.1 29.9 1.0
F4 A:2V6502 2.2 33.3 1.0
C12 A:2V6502 2.3 28.0 1.0
N4 A:2V6502 2.9 27.1 1.0
CG1 A:VAL134 3.3 39.4 1.0
N5 A:2V6502 3.3 26.1 1.0
CD1 A:ILE360 3.5 25.4 1.0
C11 A:2V6502 4.0 25.3 1.0
CG1 A:VAL143 4.1 32.1 1.0
N2 A:2V6502 4.1 25.0 1.0
CB A:PRO52 4.2 36.0 1.0
CG2 A:VAL143 4.2 26.4 1.0
CB A:VAL134 4.4 37.6 1.0
C7M A:FMN500 4.5 25.8 1.0
CG1 A:ILE360 4.5 24.0 1.0
CB A:VAL143 4.8 25.9 1.0
CG A:ARG136 4.9 33.1 1.0
OH A:TYR356 4.9 32.2 1.0
O A:PRO52 4.9 33.4 1.0
CA A:PRO52 4.9 31.5 1.0
CG2 A:ILE360 4.9 27.5 1.0

Fluorine binding site 7 out of 8 in 4ori

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Fluorine binding site 7 out of 8 in the Rat Dihydroorotate Dehydrogenase Bound with DSM338 (N-[3,5-Difluoro-4- (Trifluoromethyl)Phenyl]-5-Methyl-2-(Trifluoromethyl)[1,2, 4]Triazolo[1,5-A]Pyrimidin-7-Amine)


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 7 of Rat Dihydroorotate Dehydrogenase Bound with DSM338 (N-[3,5-Difluoro-4- (Trifluoromethyl)Phenyl]-5-Methyl-2-(Trifluoromethyl)[1,2, 4]Triazolo[1,5-A]Pyrimidin-7-Amine) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F502

b:33.3
occ:1.00
 F4 A:2V6502 0.0 33.3 1.0
C14 A:2V6502 1.3 29.0 1.0
F5 A:2V6502 2.1 29.9 1.0
F6 A:2V6502 2.2 33.8 1.0
C12 A:2V6502 2.3 28.0 1.0
N5 A:2V6502 2.6 26.1 1.0
OH A:TYR356 3.1 32.2 1.0
N4 A:2V6502 3.6 27.1 1.0
O A:HOH605 3.8 28.3 1.0
CB A:HIS56 3.9 27.1 1.0
CD1 A:ILE360 3.9 25.4 1.0
N2 A:2V6502 3.9 25.0 1.0
CZ A:TYR356 4.0 27.0 1.0
C7M A:FMN500 4.2 25.8 1.0
CG A:HIS56 4.3 32.9 1.0
ND1 A:HIS56 4.3 39.6 1.0
C11 A:2V6502 4.4 25.3 1.0
OH A:TYR147 4.4 38.2 1.0
CG1 A:ILE360 4.5 24.0 1.0
O A:PRO52 4.6 33.4 1.0
CE1 A:TYR356 4.6 25.1 1.0
CG1 A:VAL134 4.7 39.4 1.0
CA A:HIS56 4.7 28.1 1.0
CE2 A:TYR356 4.8 21.8 1.0
C8 A:2V6502 4.9 24.6 1.0

Fluorine binding site 8 out of 8 in 4ori

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Fluorine binding site 8 out of 8 in the Rat Dihydroorotate Dehydrogenase Bound with DSM338 (N-[3,5-Difluoro-4- (Trifluoromethyl)Phenyl]-5-Methyl-2-(Trifluoromethyl)[1,2, 4]Triazolo[1,5-A]Pyrimidin-7-Amine)


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 8 of Rat Dihydroorotate Dehydrogenase Bound with DSM338 (N-[3,5-Difluoro-4- (Trifluoromethyl)Phenyl]-5-Methyl-2-(Trifluoromethyl)[1,2, 4]Triazolo[1,5-A]Pyrimidin-7-Amine) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F502

b:29.9
occ:1.00
 F5 A:2V6502 0.0 29.9 1.0
C14 A:2V6502 1.3 29.0 1.0
F4 A:2V6502 2.1 33.3 1.0
F6 A:2V6502 2.1 33.8 1.0
C12 A:2V6502 2.3 28.0 1.0
N4 A:2V6502 3.0 27.1 1.0
O A:PRO52 3.1 33.4 1.0
CB A:PRO52 3.3 36.0 1.0
N5 A:2V6502 3.3 26.1 1.0
C A:PRO52 3.4 33.1 1.0
CG1 A:VAL134 3.7 39.4 1.0
CA A:PRO52 3.7 31.5 1.0
OH A:TYR147 3.7 38.2 1.0
CB A:HIS56 3.9 27.1 1.0
N A:GLU53 4.1 31.4 1.0
CB A:VAL134 4.1 37.6 1.0
C11 A:2V6502 4.1 25.3 1.0
N2 A:2V6502 4.2 25.0 1.0
CG2 A:VAL134 4.3 49.3 1.0
CA A:GLU53 4.5 36.6 1.0
CG A:PRO52 4.5 37.5 1.0
CZ A:TYR147 4.7 45.5 1.0
CG A:HIS56 4.8 32.9 1.0
N A:HIS56 4.8 27.0 1.0
CE2 A:TYR147 4.8 41.4 1.0
CA A:HIS56 4.9 28.1 1.0

Reference:

X.Deng, S.Kokkonda, F.El Mazouni, J.White, J.N.Burrows, W.Kaminsky, S.A.Charman, D.Matthews, P.K.Rathod, M.A.Phillips. Fluorine Modulates Species Selectivity in the Triazolopyrimidine Class of Plasmodium Falciparum Dihydroorotate Dehydrogenase Inhibitors. J.Med.Chem. V. 57 5381 2014.
ISSN: ISSN 0022-2623
PubMed: 24801997
DOI: 10.1021/JM500481T
Page generated: Mon Jul 14 23:57:49 2025

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