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Sodium 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:

Fluorine (F) 8 atoms

Sodium Binding Sites:

The binding sites of Sodium 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 Sodium atom.
In total 2 binding sites of Sodium 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 Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in 4oqv

Go back to Sodium Binding Sites List in 4oqv
Sodium binding site 1 out of 2 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 Sodium with other atoms in the Na 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:Na507

b:36.5
occ:1.00
 NA A:NA509 2.5 44.1 1.0
O A:HOH650 2.9 17.7 1.0
NE2 A:GLN166 3.2 23.1 1.0
CE1 A:HIS248 3.6 11.2 1.0
OE1 A:GLN166 3.9 27.4 1.0
CD A:GLN166 4.0 22.0 1.0
NE2 A:GLN165 4.0 12.8 1.0
CG A:GLN165 4.2 10.9 1.0
NE2 A:HIS248 4.2 12.4 1.0
CD A:GLN165 4.3 11.4 1.0
CG1 A:VAL247 4.3 13.3 0.5
O A:HOH933 4.3 88.4 1.0
O A:HOH660 4.5 19.2 1.0
O A:HOH642 4.5 14.6 1.0
ND1 A:HIS248 4.5 11.1 1.0
CB A:ALA169 4.7 14.3 1.0

Sodium binding site 2 out of 2 in 4oqv

Go back to Sodium Binding Sites List in 4oqv
Sodium binding site 2 out of 2 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 Sodium with other atoms in the Na 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:Na509

b:44.1
occ:1.00
 NA A:NA507 2.5 36.5 1.0
CE1 A:HIS248 3.3 11.2 1.0
O A:HOH933 3.3 88.4 1.0
NE2 A:HIS248 3.3 12.4 1.0
NE2 A:GLN166 3.4 23.1 1.0
O A:HOH911 3.6 42.1 1.0
O1 A:SO4508 3.6 30.3 1.0
NE2 A:GLN165 4.3 12.8 1.0
O A:HOH674 4.4 19.2 1.0
CD A:GLN166 4.5 22.0 1.0
ND1 A:HIS248 4.6 11.1 1.0
CD A:GLN165 4.6 11.4 1.0
CD2 A:HIS248 4.7 11.5 1.0
O A:HOH650 4.7 17.7 1.0
CG1 A:VAL247 4.8 13.3 0.5
OE1 A:GLN166 4.8 27.4 1.0
OE1 A:GLN165 4.9 12.8 1.0
O A:HOH891 4.9 53.8 1.0
O4 A:SO4508 5.0 41.1 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 Oct 7 17:32:00 2024

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