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Fluorine in PDB 7kyv: Crystal Structure of Plasmodium Falciparum Dihydroorotate Dehydrogenase Bound with Inhibitor DSM634 (3-Methyl-N-(1-(5- Methylisoxazol-3-Yl)Ethyl)-4-(4-(Trifluoromethyl)Benzyl)-1H-Pyrrole- 2-Carboxamide)

Enzymatic activity of Crystal Structure of Plasmodium Falciparum Dihydroorotate Dehydrogenase Bound with Inhibitor DSM634 (3-Methyl-N-(1-(5- Methylisoxazol-3-Yl)Ethyl)-4-(4-(Trifluoromethyl)Benzyl)-1H-Pyrrole- 2-Carboxamide)

All present enzymatic activity of Crystal Structure of Plasmodium Falciparum Dihydroorotate Dehydrogenase Bound with Inhibitor DSM634 (3-Methyl-N-(1-(5- Methylisoxazol-3-Yl)Ethyl)-4-(4-(Trifluoromethyl)Benzyl)-1H-Pyrrole- 2-Carboxamide):
1.3.5.2;

Protein crystallography data

The structure of Crystal Structure of Plasmodium Falciparum Dihydroorotate Dehydrogenase Bound with Inhibitor DSM634 (3-Methyl-N-(1-(5- Methylisoxazol-3-Yl)Ethyl)-4-(4-(Trifluoromethyl)Benzyl)-1H-Pyrrole- 2-Carboxamide), PDB code: 7kyv was solved by X.Deng, M.Phillips, D.Tomchick, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 42.64 / 2.40
Space group P 64
Cell size a, b, c (Å), α, β, γ (°) 85.288, 85.288, 139.216, 90, 90, 120
R / Rfree (%) 18 / 19.9

Fluorine Binding Sites:

The binding sites of Fluorine atom in the Crystal Structure of Plasmodium Falciparum Dihydroorotate Dehydrogenase Bound with Inhibitor DSM634 (3-Methyl-N-(1-(5- Methylisoxazol-3-Yl)Ethyl)-4-(4-(Trifluoromethyl)Benzyl)-1H-Pyrrole- 2-Carboxamide) (pdb code 7kyv). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 3 binding sites of Fluorine where determined in the Crystal Structure of Plasmodium Falciparum Dihydroorotate Dehydrogenase Bound with Inhibitor DSM634 (3-Methyl-N-(1-(5- Methylisoxazol-3-Yl)Ethyl)-4-(4-(Trifluoromethyl)Benzyl)-1H-Pyrrole- 2-Carboxamide), PDB code: 7kyv:
Jump to Fluorine binding site number: 1; 2; 3;

Fluorine binding site 1 out of 3 in 7kyv

Go back to Fluorine Binding Sites List in 7kyv
Fluorine binding site 1 out of 3 in the Crystal Structure of Plasmodium Falciparum Dihydroorotate Dehydrogenase Bound with Inhibitor DSM634 (3-Methyl-N-(1-(5- Methylisoxazol-3-Yl)Ethyl)-4-(4-(Trifluoromethyl)Benzyl)-1H-Pyrrole- 2-Carboxamide)


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 DSM634 (3-Methyl-N-(1-(5- Methylisoxazol-3-Yl)Ethyl)-4-(4-(Trifluoromethyl)Benzyl)-1H-Pyrrole- 2-Carboxamide) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F1001

b:55.3
occ:1.00
 F18 A:XBY1001 0.0 55.3 1.0
C17 A:XBY1001 1.3 47.1 1.0
F19 A:XBY1001 2.2 51.7 1.0
F20 A:XBY1001 2.2 55.4 1.0
C14 A:XBY1001 2.3 38.0 1.0
HD23 A:LEU187 2.6 45.6 1.0
HB3 A:PHE171 2.8 61.6 1.0
H131 A:XBY1001 2.9 51.5 1.0
C13 A:XBY1001 3.0 42.9 1.0
HD21 A:LEU187 3.2 45.6 1.0
C15 A:XBY1001 3.3 31.6 1.0
CD2 A:LEU187 3.3 38.1 1.0
HB2 A:CYS175 3.4 74.5 1.0
H151 A:XBY1001 3.5 37.9 1.0
CB A:PHE171 3.6 51.4 1.0
HB2 A:PHE171 3.6 61.6 1.0
O A:PHE171 3.8 49.1 1.0
SG A:CYS175 3.8 62.0 1.0
C A:PHE171 4.0 49.4 1.0
HD22 A:LEU187 4.0 45.6 1.0
HG A:LEU187 4.0 45.5 1.0
CB A:CYS175 4.1 62.1 1.0
HA A:LEU172 4.2 43.4 1.0
C12 A:XBY1001 4.2 40.9 1.0
CG A:LEU187 4.3 37.9 1.0
CA A:PHE171 4.4 50.1 1.0
HD11 A:LEU191 4.4 37.6 1.0
N A:LEU172 4.5 36.5 1.0
C16 A:XBY1001 4.5 27.5 1.0
HB3 A:CYS175 4.5 74.5 1.0
HB3 A:LEU187 4.6 44.5 1.0
HA A:PHE171 4.7 60.1 1.0
CG A:PHE171 4.7 54.4 1.0
HD12 A:LEU191 4.8 37.6 1.0
HD2 A:PHE171 4.8 65.3 1.0
C11 A:XBY1001 4.9 44.3 1.0
CA A:LEU172 4.9 36.2 1.0
H121 A:XBY1001 4.9 49.0 1.0
H A:LEU172 4.9 43.8 1.0

Fluorine binding site 2 out of 3 in 7kyv

Go back to Fluorine Binding Sites List in 7kyv
Fluorine binding site 2 out of 3 in the Crystal Structure of Plasmodium Falciparum Dihydroorotate Dehydrogenase Bound with Inhibitor DSM634 (3-Methyl-N-(1-(5- Methylisoxazol-3-Yl)Ethyl)-4-(4-(Trifluoromethyl)Benzyl)-1H-Pyrrole- 2-Carboxamide)


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 DSM634 (3-Methyl-N-(1-(5- Methylisoxazol-3-Yl)Ethyl)-4-(4-(Trifluoromethyl)Benzyl)-1H-Pyrrole- 2-Carboxamide) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F1001

b:51.7
occ:1.00
 F19 A:XBY1001 0.0 51.7 1.0
C17 A:XBY1001 1.3 47.1 1.0
F18 A:XBY1001 2.2 55.3 1.0
F20 A:XBY1001 2.2 55.4 1.0
C14 A:XBY1001 2.3 38.0 1.0
HG A:LEU187 2.4 45.5 1.0
HD11 A:LEU191 2.5 37.6 1.0
HD23 A:LEU187 2.6 45.6 1.0
H131 A:XBY1001 2.6 51.5 1.0
HD12 A:LEU191 2.7 37.6 1.0
C13 A:XBY1001 2.8 42.9 1.0
HD21 A:LEU187 2.9 45.6 1.0
CD2 A:LEU187 3.0 38.1 1.0
CD1 A:LEU191 3.0 31.3 1.0
CG A:LEU187 3.1 37.9 1.0
C15 A:XBY1001 3.4 31.6 1.0
HD13 A:LEU191 3.5 37.6 1.0
H151 A:XBY1001 3.6 37.9 1.0
HB3 A:LEU187 3.7 44.5 1.0
HD22 A:LEU187 3.9 45.6 1.0
CB A:LEU187 4.0 37.1 1.0
HA A:PHE188 4.1 30.7 1.0
C12 A:XBY1001 4.1 40.9 1.0
HG A:LEU191 4.2 36.9 1.0
HD11 A:LEU187 4.2 45.6 1.0
CG A:LEU191 4.2 30.7 1.0
HB3 A:PHE171 4.2 61.6 1.0
HE1 A:TYR168 4.2 42.5 1.0
CD1 A:LEU187 4.3 38.0 1.0
N A:PHE188 4.3 27.0 1.0
H A:PHE188 4.4 32.4 1.0
HD1 A:TYR168 4.4 43.1 1.0
C A:LEU187 4.4 30.3 1.0
HD21 A:LEU191 4.5 39.2 1.0
C16 A:XBY1001 4.5 27.5 1.0
HD12 A:LEU187 4.6 45.6 1.0
HB2 A:PHE171 4.6 61.6 1.0
CA A:PHE188 4.7 25.6 1.0
O A:LEU187 4.7 29.2 1.0
H121 A:XBY1001 4.7 49.0 1.0
HB2 A:LEU187 4.8 44.5 1.0
C11 A:XBY1001 4.8 44.3 1.0
CA A:LEU187 4.9 31.7 1.0
CB A:PHE171 4.9 51.4 1.0
HE3 A:MET536 4.9 45.3 1.0
CD2 A:LEU191 4.9 32.7 1.0
O A:CYS184 4.9 32.2 1.0
HD2 A:PHE171 5.0 65.3 1.0
CE1 A:TYR168 5.0 35.4 1.0
HB2 A:PHE188 5.0 31.4 1.0

Fluorine binding site 3 out of 3 in 7kyv

Go back to Fluorine Binding Sites List in 7kyv
Fluorine binding site 3 out of 3 in the Crystal Structure of Plasmodium Falciparum Dihydroorotate Dehydrogenase Bound with Inhibitor DSM634 (3-Methyl-N-(1-(5- Methylisoxazol-3-Yl)Ethyl)-4-(4-(Trifluoromethyl)Benzyl)-1H-Pyrrole- 2-Carboxamide)


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 DSM634 (3-Methyl-N-(1-(5- Methylisoxazol-3-Yl)Ethyl)-4-(4-(Trifluoromethyl)Benzyl)-1H-Pyrrole- 2-Carboxamide) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F1001

b:55.4
occ:1.00
 F20 A:XBY1001 0.0 55.4 1.0
C17 A:XBY1001 1.3 47.1 1.0
F18 A:XBY1001 2.2 55.3 1.0
F19 A:XBY1001 2.2 51.7 1.0
H151 A:XBY1001 2.3 37.9 1.0
C14 A:XBY1001 2.3 38.0 1.0
HB2 A:PHE171 2.5 61.6 1.0
C15 A:XBY1001 2.6 31.6 1.0
HB3 A:PHE171 2.7 61.6 1.0
HD1 A:TYR168 2.8 43.1 1.0
CB A:PHE171 3.0 51.4 1.0
HD2 A:PHE171 3.2 65.3 1.0
HD11 A:LEU191 3.5 37.6 1.0
C13 A:XBY1001 3.6 42.9 1.0
HE1 A:TYR168 3.6 42.5 1.0
CD1 A:TYR168 3.6 35.9 1.0
CD2 A:PHE171 3.8 54.4 1.0
CG A:PHE171 3.8 54.4 1.0
H131 A:XBY1001 3.9 51.5 1.0
C16 A:XBY1001 4.0 27.5 1.0
HD12 A:LEU191 4.0 37.6 1.0
CE1 A:TYR168 4.1 35.4 1.0
CD1 A:LEU191 4.1 31.3 1.0
HD13 A:LEU191 4.1 37.6 1.0
C A:PHE171 4.2 49.4 1.0
CA A:PHE171 4.2 50.1 1.0
HD23 A:LEU187 4.2 45.6 1.0
HA A:TYR168 4.3 45.6 1.0
HD21 A:LEU187 4.3 45.6 1.0
HE3 A:MET536 4.3 45.3 1.0
O A:TYR168 4.3 42.7 1.0
N A:LEU172 4.4 36.5 1.0
H A:LEU172 4.4 43.8 1.0
H161 A:XBY1001 4.6 33.0 1.0
HG A:LEU187 4.6 45.5 1.0
HE2 A:MET536 4.6 45.3 1.0
HA A:LEU172 4.6 43.4 1.0
O A:PHE171 4.6 49.1 1.0
CD2 A:LEU187 4.7 38.1 1.0
C12 A:XBY1001 4.7 40.9 1.0
CE A:MET536 4.8 37.8 1.0
HB3 A:TYR168 4.8 43.5 1.0
HA A:PHE171 4.8 60.1 1.0
CG A:TYR168 4.8 34.3 1.0
C11 A:XBY1001 4.8 44.3 1.0
HE1 A:MET536 4.9 45.3 1.0
H A:PHE171 5.0 62.2 1.0
CA A:TYR168 5.0 38.0 1.0

Reference:

M.Palmer, X.Deng, S.Watts, G.Krilov, A.Gerasyuto, S.Kokkonda, F.Mazouni, J.White, K.Schindler, J.Striepen, K.White, D.Shackleford, J.Bath, A.Lawong, A.Huang, D.Tomchick, S.Charman, M.Phillips. Structure-Guided Optimization of Pyrrole-Based Dihydroorotate Dehydrogenase Inhibitor Series Identifies Compounds with Preclinical Candidate Potential For Treatment of Malaria To Be Published.
Page generated: Fri Aug 2 08:39:13 2024

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