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Fluorine in PDB 4oqv: High Resolution Crystal Structure of Human 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 High Resolution Crystal Structure of Human 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 High Resolution Crystal Structure of Human 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 High Resolution Crystal Structure of Human 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: 4oqv 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) 30.00 / 1.23
Space group P 32 2 1
Cell size a, b, c (Å), α, β, γ (°) 90.936, 90.936, 121.938, 90.00, 90.00, 120.00
R / Rfree (%) 14.1 / 15.7

Other elements in 4oqv:

The structure of High Resolution Crystal Structure of Human 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) also contains other interesting chemical elements:

Sodium (Na) 2 atoms

Fluorine Binding Sites:

The binding sites of Fluorine atom in the High Resolution Crystal Structure of Human 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 4oqv). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 8 binding sites of Fluorine where determined in the High Resolution Crystal Structure of Human 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: 4oqv:
Jump to Fluorine binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Fluorine binding site 1 out of 8 in 4oqv

Go back to Fluorine Binding Sites List in 4oqv
Fluorine binding site 1 out of 8 in the High Resolution Crystal Structure of Human 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 High Resolution Crystal Structure of Human 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:F503

b:28.5
occ:1.00
 F8 A:2V6503 0.0 28.5 1.0
C5 A:2V6503 1.3 24.9 1.0
C6 A:2V6503 2.3 21.9 1.0
F1 A:2V6503 2.3 81.2 1.0
C4 A:2V6503 2.4 26.9 1.0
C7 A:2V6503 2.8 49.2 1.0
CD A:PRO364 3.5 17.5 1.0
C1 A:2V6503 3.6 17.4 1.0
C3 A:2V6503 3.6 21.3 1.0
CG A:LEU359 3.7 14.3 1.0
F2 A:2V6503 3.7 47.4 1.0
CD1 A:LEU359 3.8 17.0 1.0
F3 A:2V6503 3.9 28.8 1.0
CG A:PRO364 3.9 20.1 1.0
O A:LEU359 4.0 13.7 1.0
C2 A:2V6503 4.1 19.7 1.0
CD2 A:LEU359 4.1 19.3 1.0
CA A:GLY363 4.2 16.3 1.0
N A:PRO364 4.2 16.0 1.0
CB A:ALA59 4.4 16.3 1.0
C A:GLY363 4.5 15.4 1.0
CE A:MET43 4.6 22.7 1.0
N1 A:2V6503 4.7 19.4 1.0
F7 A:2V6503 4.8 22.7 1.0
C A:LEU359 4.8 12.9 1.0
CB A:LEU359 5.0 13.7 1.0
CE A:MET111 5.0 25.6 1.0

Fluorine binding site 2 out of 8 in 4oqv

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Fluorine binding site 2 out of 8 in the High Resolution Crystal Structure of Human 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 High Resolution Crystal Structure of Human 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:F503

b:28.8
occ:1.00
 F3 A:2V6503 0.0 28.8 1.0
C7 A:2V6503 1.3 49.2 1.0
F2 A:2V6503 2.1 47.4 1.0
F1 A:2V6503 2.2 81.2 1.0
C4 A:2V6503 2.3 26.9 1.0
F7 A:2V6503 2.8 22.7 1.0
C3 A:2V6503 2.8 21.3 1.0
C5 A:2V6503 3.5 24.9 1.0
CD2 A:LEU68 3.8 40.8 1.0
CA A:ALA59 3.9 14.5 1.0
F8 A:2V6503 3.9 28.5 1.0
CB A:PHE62 4.1 22.0 1.0
CB A:ALA59 4.2 16.3 1.0
C2 A:2V6503 4.2 19.7 1.0
CD1 A:LEU68 4.2 38.8 1.0
CG A:PHE62 4.5 30.9 1.0
CG A:LEU68 4.6 33.1 1.0
O A:ALA59 4.6 16.2 1.0
C6 A:2V6503 4.7 21.9 1.0
N A:ALA59 4.7 14.1 1.0
CD2 A:PHE62 4.8 40.5 1.0
C A:ALA59 4.8 14.3 1.0
C1 A:2V6503 4.9 17.4 1.0
O A:LEU58 5.0 17.4 1.0

Fluorine binding site 3 out of 8 in 4oqv

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Fluorine binding site 3 out of 8 in the High Resolution Crystal Structure of Human 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 High Resolution Crystal Structure of Human 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:F503

b:47.4
occ:1.00
 F2 A:2V6503 0.0 47.4 1.0
C7 A:2V6503 1.3 49.2 1.0
F3 A:2V6503 2.1 28.8 1.0
F1 A:2V6503 2.2 81.2 1.0
C4 A:2V6503 2.3 26.9 1.0
C3 A:2V6503 3.0 21.3 1.0
F7 A:2V6503 3.1 22.7 1.0
C5 A:2V6503 3.4 24.9 1.0
F8 A:2V6503 3.7 28.5 1.0
CE1 A:TYR38 3.9 0.8 1.0
CD A:PRO364 4.0 17.5 1.0
CD1 A:LEU42 4.2 49.2 1.0
C2 A:2V6503 4.3 19.7 1.0
CD2 A:LEU68 4.3 40.8 1.0
SD A:MET43 4.3 25.5 1.0
CG A:PRO364 4.4 20.1 1.0
C6 A:2V6503 4.6 21.9 1.0
OH A:TYR38 4.6 0.2 1.0
CD1 A:TYR38 4.7 59.6 1.0
CZ A:TYR38 4.7 71.1 1.0
CE A:MET43 4.9 22.7 1.0
CD1 A:LEU46 4.9 47.9 1.0
C1 A:2V6503 4.9 17.4 1.0

Fluorine binding site 4 out of 8 in 4oqv

Go back to Fluorine Binding Sites List in 4oqv
Fluorine binding site 4 out of 8 in the High Resolution Crystal Structure of Human 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 High Resolution Crystal Structure of Human 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:F503

b:81.2
occ:1.00
 F1 A:2V6503 0.0 81.2 1.0
C7 A:2V6503 1.3 49.2 1.0
F3 A:2V6503 2.2 28.8 1.0
F2 A:2V6503 2.2 47.4 1.0
C4 A:2V6503 2.3 26.9 1.0
F8 A:2V6503 2.3 28.5 1.0
C5 A:2V6503 2.7 24.9 1.0
CG A:PRO364 3.2 20.1 1.0
CD A:PRO364 3.3 17.5 1.0
CD1 A:LEU68 3.5 38.8 1.0
C3 A:2V6503 3.6 21.3 1.0
CD2 A:LEU68 4.0 40.8 1.0
C6 A:2V6503 4.1 21.9 1.0
F7 A:2V6503 4.2 22.7 1.0
CG A:LEU68 4.4 33.1 1.0
N A:PRO364 4.6 16.0 1.0
C2 A:2V6503 4.7 19.7 1.0
CB A:PRO364 4.7 18.8 1.0
CB A:ALA59 4.7 16.3 1.0
OG1 A:THR63 4.8 16.9 1.0
CE A:MET111 4.8 25.6 1.0
C1 A:2V6503 4.9 17.4 1.0
CE1 A:TYR38 5.0 0.8 1.0

Fluorine binding site 5 out of 8 in 4oqv

Go back to Fluorine Binding Sites List in 4oqv
Fluorine binding site 5 out of 8 in the High Resolution Crystal Structure of Human 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 High Resolution Crystal Structure of Human 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:F503

b:22.7
occ:1.00
 F7 A:2V6503 0.0 22.7 1.0
C3 A:2V6503 1.4 21.3 1.0
C2 A:2V6503 2.3 19.7 1.0
C4 A:2V6503 2.4 26.9 1.0
F3 A:2V6503 2.8 28.8 1.0
C7 A:2V6503 2.9 49.2 1.0
F2 A:2V6503 3.1 47.4 1.0
CD1 A:LEU46 3.3 47.9 1.0
C1 A:2V6503 3.6 17.4 1.0
C5 A:2V6503 3.7 24.9 1.0
CA A:ALA59 4.1 14.5 1.0
CB A:ALA59 4.1 16.3 1.0
C6 A:2V6503 4.2 21.9 1.0
N A:ALA59 4.2 14.1 1.0
F1 A:2V6503 4.2 81.2 1.0
O A:ALA55 4.3 14.6 1.0
CD2 A:LEU58 4.4 34.4 1.0
CG A:LEU58 4.5 25.0 1.0
CG A:LEU46 4.7 36.4 1.0
N1 A:2V6503 4.7 19.4 1.0
F8 A:2V6503 4.8 28.5 1.0
C A:LEU58 4.8 15.2 1.0
CB A:LEU58 4.8 19.5 1.0
CD1 A:LEU42 4.8 49.2 1.0
C9 A:2V6503 5.0 18.3 1.0

Fluorine binding site 6 out of 8 in 4oqv

Go back to Fluorine Binding Sites List in 4oqv
Fluorine binding site 6 out of 8 in the High Resolution Crystal Structure of Human 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 High Resolution Crystal Structure of Human 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:F503

b:19.2
occ:1.00
 F6 A:2V6503 0.0 19.2 1.0
C14 A:2V6503 1.3 19.2 1.0
F5 A:2V6503 2.1 20.4 1.0
F4 A:2V6503 2.2 22.8 1.0
C12 A:2V6503 2.3 17.1 1.0
N4 A:2V6503 2.8 18.0 1.0
CG1 A:VAL134 3.3 8.8 0.5
N5 A:2V6503 3.4 17.3 1.0
CG2 A:VAL134 3.7 8.5 0.5
CG1 A:VAL143 3.7 9.8 1.0
CG2 A:VAL143 3.9 10.2 1.0
CB A:PRO52 4.0 16.4 1.0
C11 A:2V6503 4.0 18.8 1.0
O A:HOH710 4.1 20.8 1.0
N2 A:2V6503 4.3 17.3 1.0
CG2 A:THR360 4.3 15.8 1.0
CB A:VAL143 4.4 8.3 1.0
C7M A:FMN501 4.5 12.1 1.0
CB A:THR360 4.6 16.4 1.0
CB A:VAL134 4.7 8.2 0.5
O A:PRO52 4.7 12.8 1.0
OG1 A:THR360 4.8 17.1 1.0
CA A:PRO52 4.9 14.1 1.0
C A:PRO52 4.9 12.4 1.0
OH A:TYR356 4.9 20.1 1.0
CB A:VAL134 4.9 9.6 0.5
CG1 A:VAL134 5.0 10.9 0.5

Fluorine binding site 7 out of 8 in 4oqv

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Fluorine binding site 7 out of 8 in the High Resolution Crystal Structure of Human 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 High Resolution Crystal Structure of Human 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:F503

b:22.8
occ:1.00
 F4 A:2V6503 0.0 22.8 1.0
C14 A:2V6503 1.3 19.2 1.0
F5 A:2V6503 2.2 20.4 1.0
F6 A:2V6503 2.2 19.2 1.0
C12 A:2V6503 2.4 17.1 1.0
N5 A:2V6503 2.6 17.3 1.0
OH A:TYR356 2.9 20.1 1.0
N4 A:2V6503 3.6 18.0 1.0
CZ A:TYR356 3.6 15.2 1.0
O A:HOH675 3.7 19.9 1.0
CG2 A:THR360 3.8 15.8 1.0
CB A:HIS56 3.9 12.8 1.0
N2 A:2V6503 4.0 17.3 1.0
C7M A:FMN501 4.1 12.1 1.0
CE1 A:TYR356 4.1 14.9 1.0
O A:HOH691 4.1 23.2 1.0
CG A:HIS56 4.2 12.9 1.0
ND1 A:HIS56 4.3 15.8 1.0
C11 A:2V6503 4.4 18.8 1.0
CE2 A:TYR356 4.5 13.0 1.0
CG1 A:VAL134 4.6 8.8 0.5
O A:PRO52 4.6 12.8 1.0
CB A:THR360 4.7 16.4 1.0
CG2 A:VAL134 4.9 8.5 0.5
CA A:HIS56 4.9 12.1 1.0
C8 A:2V6503 5.0 18.6 1.0
OH A:TYR147 5.0 14.8 0.5

Fluorine binding site 8 out of 8 in 4oqv

Go back to Fluorine Binding Sites List in 4oqv
Fluorine binding site 8 out of 8 in the High Resolution Crystal Structure of Human 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 High Resolution Crystal Structure of Human 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:F503

b:20.4
occ:1.00
 F5 A:2V6503 0.0 20.4 1.0
C14 A:2V6503 1.3 19.2 1.0
F6 A:2V6503 2.1 19.2 1.0
F4 A:2V6503 2.2 22.8 1.0
C12 A:2V6503 2.3 17.1 1.0
O A:PRO52 3.1 12.8 1.0
N4 A:2V6503 3.1 18.0 1.0
CG1 A:VAL134 3.2 8.8 0.5
N5 A:2V6503 3.3 17.3 1.0
C A:PRO52 3.3 12.4 1.0
CB A:PRO52 3.4 16.4 1.0
CG2 A:VAL134 3.7 8.5 0.5
CG1 A:VAL134 3.8 10.9 0.5
N A:GLU53 3.8 12.7 1.0
CA A:PRO52 3.8 14.1 1.0
CB A:HIS56 3.9 12.8 1.0
CB A:VAL134 4.0 8.2 0.5
OH A:TYR147 4.0 14.8 0.5
CA A:GLU53 4.1 12.2 1.0
C11 A:2V6503 4.2 18.8 1.0
N2 A:2V6503 4.3 17.3 1.0
CB A:VAL134 4.3 9.6 0.5
CG2 A:VAL134 4.4 10.0 0.5
CG A:PRO52 4.6 19.6 1.0
OH A:TYR147 4.7 11.9 0.5
OH A:TYR356 4.8 20.1 1.0
CG A:HIS56 4.8 12.9 1.0
C7M A:FMN501 4.8 12.1 1.0
N A:HIS56 4.9 12.5 1.0
CE2 A:TYR147 4.9 11.6 0.5
CZ A:TYR147 4.9 13.2 0.5
CA A:HIS56 4.9 12.1 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: Thu Aug 1 04:39:35 2024

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