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Fluorine in PDB 4orm: Crystal Structure of Plasmodium Falciparum Dihydroorotate Dehydrogenase Bound with Inhibitor 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 Crystal Structure of Plasmodium Falciparum Dihydroorotate Dehydrogenase Bound with Inhibitor 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 Crystal Structure of Plasmodium Falciparum Dihydroorotate Dehydrogenase Bound with Inhibitor 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 Crystal Structure of Plasmodium Falciparum Dihydroorotate Dehydrogenase Bound with Inhibitor DSM338 (N-[3,5-Difluoro-4- (Trifluoromethyl)Phenyl]-5-Methyl-2-(Trifluoromethyl)[1,2, 4]Triazolo[1,5-A]Pyrimidin-7-Amine), PDB code: 4orm 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) 28.00 / 2.07
Space group P 64
Cell size a, b, c (Å), α, β, γ (°) 85.471, 85.471, 138.275, 90.00, 90.00, 120.00
R / Rfree (%) 18.6 / 24

Fluorine Binding Sites:

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

Fluorine binding site 1 out of 8 in 4orm

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Fluorine binding site 1 out of 8 in the Crystal Structure of Plasmodium Falciparum Dihydroorotate Dehydrogenase Bound with Inhibitor 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 Crystal Structure of Plasmodium Falciparum Dihydroorotate Dehydrogenase Bound with Inhibitor 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:F1001

b:39.0
occ:1.00
 F8 A:2V61001 0.0 39.0 1.0
C5 A:2V61001 1.3 36.3 1.0
C6 A:2V61001 2.4 38.0 1.0
C4 A:2V61001 2.4 35.4 1.0
F1 A:2V61001 2.4 44.2 1.0
C7 A:2V61001 2.8 44.2 1.0
O A:LEU531 3.3 39.6 1.0
CD1 A:LEU172 3.5 44.1 1.0
F2 A:2V61001 3.6 44.4 1.0
C1 A:2V61001 3.6 36.2 1.0
C3 A:2V61001 3.7 30.1 1.0
F3 A:2V61001 3.9 41.4 1.0
CB A:LEU531 3.9 35.6 1.0
CD2 A:LEU531 4.0 36.5 1.0
C A:GLY535 4.0 43.0 1.0
C A:LEU531 4.0 40.5 1.0
N A:MET536 4.1 39.7 1.0
CA A:GLY535 4.1 40.8 1.0
C2 A:2V61001 4.2 37.7 1.0
CA A:LEU531 4.3 38.0 1.0
O A:GLY535 4.4 44.8 1.0
CG A:MET536 4.4 46.8 1.0
CA A:MET536 4.5 44.9 1.0
CG A:LEU531 4.5 40.4 1.0
F7 A:2V61001 4.8 35.4 1.0
N1 A:2V61001 4.8 39.9 1.0
CZ A:PHE227 4.9 29.9 1.0
CG A:LEU172 4.9 46.0 1.0
CE A:MET536 4.9 45.4 1.0
N A:GLY535 5.0 46.0 1.0
N A:VAL532 5.0 40.0 1.0

Fluorine binding site 2 out of 8 in 4orm

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Fluorine binding site 2 out of 8 in the Crystal Structure of Plasmodium Falciparum Dihydroorotate Dehydrogenase Bound with Inhibitor 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 Crystal Structure of Plasmodium Falciparum Dihydroorotate Dehydrogenase Bound with Inhibitor 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:F1001

b:41.4
occ:1.00
 F3 A:2V61001 0.0 41.4 1.0
C7 A:2V61001 1.3 44.2 1.0
F2 A:2V61001 2.0 44.4 1.0
F1 A:2V61001 2.1 44.2 1.0
C4 A:2V61001 2.3 35.4 1.0
F7 A:2V61001 2.7 35.4 1.0
C3 A:2V61001 2.8 30.1 1.0
C5 A:2V61001 3.5 36.3 1.0
CD1 A:LEU240 3.6 34.5 1.0
CE1 A:PHE227 3.8 34.2 1.0
F8 A:2V61001 3.9 39.0 1.0
CG1 A:ILE237 4.0 33.5 1.0
CZ A:PHE227 4.2 29.9 1.0
C2 A:2V61001 4.2 37.7 1.0
CD1 A:LEU197 4.6 37.0 1.0
C6 A:2V61001 4.7 38.0 1.0
CD2 A:LEU531 4.7 36.5 1.0
CD1 A:ILE237 4.7 32.3 1.0
C1 A:2V61001 4.9 36.2 1.0
CB A:ILE237 5.0 33.8 1.0
CD1 A:PHE227 5.0 32.0 1.0

Fluorine binding site 3 out of 8 in 4orm

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Fluorine binding site 3 out of 8 in the Crystal Structure of Plasmodium Falciparum Dihydroorotate Dehydrogenase Bound with Inhibitor 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 Crystal Structure of Plasmodium Falciparum Dihydroorotate Dehydrogenase Bound with Inhibitor 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:F1001

b:44.4
occ:1.00
 F2 A:2V61001 0.0 44.4 1.0
C7 A:2V61001 1.3 44.2 1.0
F1 A:2V61001 2.0 44.2 1.0
F3 A:2V61001 2.0 41.4 1.0
C4 A:2V61001 2.4 35.4 1.0
F7 A:2V61001 3.1 35.4 1.0
C3 A:2V61001 3.1 30.1 1.0
CD1 A:LEU197 3.3 37.0 1.0
C5 A:2V61001 3.4 36.3 1.0
F8 A:2V61001 3.6 39.0 1.0
CE A:MET536 3.9 45.4 1.0
CG A:MET536 3.9 46.8 1.0
CB A:PHE188 4.0 42.9 1.0
CD1 A:LEU240 4.1 34.5 1.0
C2 A:2V61001 4.4 37.7 1.0
SD A:MET536 4.5 47.0 1.0
O A:PHE188 4.6 38.3 1.0
CG A:PHE188 4.6 46.1 1.0
CG A:LEU197 4.6 40.7 1.0
C6 A:2V61001 4.6 38.0 1.0
CD1 A:PHE188 4.6 42.8 1.0
C A:PHE188 4.8 38.0 1.0
CD2 A:LEU197 4.8 43.6 1.0
CA A:PHE188 4.8 39.9 1.0
C1 A:2V61001 5.0 36.2 1.0

Fluorine binding site 4 out of 8 in 4orm

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Fluorine binding site 4 out of 8 in the Crystal Structure of Plasmodium Falciparum Dihydroorotate Dehydrogenase Bound with Inhibitor 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 Crystal Structure of Plasmodium Falciparum Dihydroorotate Dehydrogenase Bound with Inhibitor 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:F1001

b:44.2
occ:1.00
 F1 A:2V61001 0.0 44.2 1.0
C7 A:2V61001 1.3 44.2 1.0
F2 A:2V61001 2.0 44.4 1.0
F3 A:2V61001 2.1 41.4 1.0
C4 A:2V61001 2.4 35.4 1.0
F8 A:2V61001 2.4 39.0 1.0
C5 A:2V61001 2.8 36.3 1.0
CD1 A:LEU240 3.3 34.5 1.0
CG A:MET536 3.4 46.8 1.0
C3 A:2V61001 3.7 30.1 1.0
CD2 A:LEU531 3.8 36.5 1.0
CA A:MET536 4.1 44.9 1.0
F7 A:2V61001 4.2 35.4 1.0
C6 A:2V61001 4.2 38.0 1.0
CB A:MET536 4.4 46.0 1.0
CE A:MET536 4.5 45.4 1.0
N A:MET536 4.5 39.7 1.0
SD A:MET536 4.7 47.0 1.0
CG A:LEU240 4.7 31.4 1.0
CG A:LEU531 4.8 40.4 1.0
C2 A:2V61001 4.8 37.7 1.0
C A:GLY535 4.8 43.0 1.0
CD1 A:LEU197 4.9 37.0 1.0
CD2 A:LEU240 4.9 33.4 1.0
CB A:LEU531 4.9 35.6 1.0

Fluorine binding site 5 out of 8 in 4orm

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Fluorine binding site 5 out of 8 in the Crystal Structure of Plasmodium Falciparum Dihydroorotate Dehydrogenase Bound with Inhibitor 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 Crystal Structure of Plasmodium Falciparum Dihydroorotate Dehydrogenase Bound with Inhibitor 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:F1001

b:35.4
occ:1.00
 F7 A:2V61001 0.0 35.4 1.0
C3 A:2V61001 1.3 30.1 1.0
C2 A:2V61001 2.3 37.7 1.0
C4 A:2V61001 2.4 35.4 1.0
F3 A:2V61001 2.7 41.4 1.0
C7 A:2V61001 2.9 44.2 1.0
F2 A:2V61001 3.1 44.4 1.0
CB A:PHE188 3.5 42.9 1.0
CE1 A:PHE227 3.5 34.2 1.0
N A:LEU189 3.6 34.9 1.0
C1 A:2V61001 3.6 36.2 1.0
C A:PHE188 3.6 38.0 1.0
C5 A:2V61001 3.7 36.3 1.0
CD2 A:LEU189 3.8 36.2 1.0
O A:PHE188 4.0 38.3 1.0
CZ A:PHE227 4.1 29.9 1.0
CA A:PHE188 4.1 39.9 1.0
CG A:LEU189 4.1 34.0 1.0
CA A:LEU189 4.2 39.6 1.0
F1 A:2V61001 4.2 44.2 1.0
C6 A:2V61001 4.2 38.0 1.0
O A:HIS185 4.3 36.5 1.0
CD1 A:PHE227 4.6 32.0 1.0
N1 A:2V61001 4.6 39.9 1.0
CB A:LEU189 4.7 34.3 1.0
CG A:PHE188 4.7 46.1 1.0
F8 A:2V61001 4.8 39.0 1.0
CE1 A:HIS185 4.9 47.2 1.0
CG1 A:ILE237 4.9 33.5 1.0
ND1 A:HIS185 4.9 44.2 1.0
CD1 A:ILE237 5.0 32.3 1.0

Fluorine binding site 6 out of 8 in 4orm

Go back to Fluorine Binding Sites List in 4orm
Fluorine binding site 6 out of 8 in the Crystal Structure of Plasmodium Falciparum Dihydroorotate Dehydrogenase Bound with Inhibitor 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 Crystal Structure of Plasmodium Falciparum Dihydroorotate Dehydrogenase Bound with Inhibitor 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:F1001

b:42.9
occ:1.00
 F6 A:2V61001 0.0 42.9 1.0
C14 A:2V61001 1.3 46.0 1.0
F4 A:2V61001 2.1 46.1 1.0
F5 A:2V61001 2.2 46.8 1.0
C12 A:2V61001 2.3 46.9 1.0
N4 A:2V61001 3.1 41.1 1.0
N5 A:2V61001 3.1 37.2 1.0
CG2 A:ILE263 3.4 39.4 1.0
CG2 A:ILE272 3.8 43.3 1.0
CD1 A:ILE272 3.8 41.8 1.0
N2 A:2V61001 4.1 44.3 1.0
C11 A:2V61001 4.1 44.8 1.0
CG2 A:VAL532 4.2 41.4 1.0
CB A:ILE263 4.4 41.9 1.0
CG1 A:ILE272 4.5 40.8 1.0
CD A:ARG265 4.6 44.9 1.0
CD1 A:ILE263 4.6 36.2 1.0
CG1 A:VAL532 4.7 42.9 1.0
C7M A:FMN1002 4.7 39.2 1.0
CB A:ILE272 4.8 43.6 1.0
CE1 A:TYR528 4.9 40.3 1.0
CA A:GLY181 4.9 43.3 1.0
NE A:ARG265 4.9 45.7 1.0

Fluorine binding site 7 out of 8 in 4orm

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Fluorine binding site 7 out of 8 in the Crystal Structure of Plasmodium Falciparum Dihydroorotate Dehydrogenase Bound with Inhibitor 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 Crystal Structure of Plasmodium Falciparum Dihydroorotate Dehydrogenase Bound with Inhibitor 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:F1001

b:46.1
occ:1.00
 F4 A:2V61001 0.0 46.1 1.0
C14 A:2V61001 1.3 46.0 1.0
F6 A:2V61001 2.1 42.9 1.0
F5 A:2V61001 2.1 46.8 1.0
C12 A:2V61001 2.3 46.9 1.0
N5 A:2V61001 2.5 37.2 1.0
N4 A:2V61001 3.6 41.1 1.0
CD1 A:ILE263 3.7 36.2 1.0
N2 A:2V61001 3.8 44.3 1.0
CB A:HIS185 3.9 38.1 1.0
CG A:HIS185 3.9 44.6 1.0
ND1 A:HIS185 4.0 44.2 1.0
CG2 A:ILE263 4.0 39.4 1.0
OH A:TYR528 4.1 44.0 1.0
C7M A:FMN1002 4.2 39.2 1.0
C11 A:2V61001 4.3 44.8 1.0
O A:GLY181 4.3 44.3 1.0
C A:GLY181 4.4 42.7 1.0
CE1 A:TYR528 4.6 40.3 1.0
CB A:ILE263 4.6 41.9 1.0
CD2 A:HIS185 4.6 43.0 1.0
CG1 A:ILE263 4.7 43.3 1.0
CE1 A:HIS185 4.7 47.2 1.0
N A:GLU182 4.8 43.1 1.0
C8 A:2V61001 4.8 43.1 1.0
CZ A:TYR528 4.8 38.8 1.0
CG2 A:VAL532 4.8 41.4 1.0
CA A:GLU182 4.9 44.1 1.0
CA A:GLY181 5.0 43.3 1.0

Fluorine binding site 8 out of 8 in 4orm

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Fluorine binding site 8 out of 8 in the Crystal Structure of Plasmodium Falciparum Dihydroorotate Dehydrogenase Bound with Inhibitor 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 Crystal Structure of Plasmodium Falciparum Dihydroorotate Dehydrogenase Bound with Inhibitor 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:F1001

b:46.8
occ:1.00
 F5 A:2V61001 0.0 46.8 1.0
C14 A:2V61001 1.3 46.0 1.0
F4 A:2V61001 2.1 46.1 1.0
F6 A:2V61001 2.2 42.9 1.0
C12 A:2V61001 2.2 46.9 1.0
N4 A:2V61001 2.8 41.1 1.0
C A:GLY181 3.0 42.7 1.0
CA A:GLY181 3.2 43.3 1.0
N5 A:2V61001 3.2 37.2 1.0
N A:GLU182 3.3 43.1 1.0
CG2 A:ILE263 3.4 39.4 1.0
O A:GLY181 3.4 44.3 1.0
CB A:ILE263 3.6 41.9 1.0
CD1 A:ILE263 3.6 36.2 1.0
CA A:GLU182 4.0 44.1 1.0
C11 A:2V61001 4.0 44.8 1.0
N2 A:2V61001 4.1 44.3 1.0
CG1 A:ILE263 4.2 43.3 1.0
N A:GLY181 4.5 40.3 1.0
CB A:HIS185 4.6 38.1 1.0
CD A:ARG265 4.7 44.9 1.0
O A:ILE263 4.7 43.3 1.0
NE A:ARG265 4.7 45.7 1.0
O A:HOH1141 4.7 41.2 1.0
CB A:GLU182 4.7 42.6 1.0
C A:ILE263 4.9 43.2 1.0
CA A:ILE263 4.9 42.3 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: Thu Aug 1 04:40:28 2024

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