Atomistry » Fluorine » PDB 4olm-4pa0 » 4orm
Atomistry »
  Fluorine »
    PDB 4olm-4pa0 »
      4orm »

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

Go back to Fluorine Binding Sites List in 4orm
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

Go back to Fluorine Binding Sites List in 4orm
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

Go back to Fluorine Binding Sites List in 4orm
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

Go back to Fluorine Binding Sites List in 4orm
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

Go back to Fluorine Binding Sites List in 4orm
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

Go back to Fluorine Binding Sites List in 4orm
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

Go back to Fluorine Binding Sites List in 4orm
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: Sun Dec 13 12:10:00 2020

Last articles

Zn in 8WB0
Zn in 8WAX
Zn in 8WAU
Zn in 8WAZ
Zn in 8WAY
Zn in 8WAV
Zn in 8WAW
Zn in 8WAT
Zn in 8W7M
Zn in 8WD3
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy