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Fluorine in PDB 7kz4: Crystal Structure of Plasmodium Falciparum Dihydroorotate Dehydrogenase Bound with Inhibitor DSM705 (N-(1-(1H-1,2,4-Triazol-3- Yl)Ethyl)-3-Methyl-4-(1-(6-(Trifluoromethyl)Pyridin-3-Yl) Cyclopropyl)-1H-Pyrrole-2-Carboxamide)

Enzymatic activity of Crystal Structure of Plasmodium Falciparum Dihydroorotate Dehydrogenase Bound with Inhibitor DSM705 (N-(1-(1H-1,2,4-Triazol-3- Yl)Ethyl)-3-Methyl-4-(1-(6-(Trifluoromethyl)Pyridin-3-Yl) Cyclopropyl)-1H-Pyrrole-2-Carboxamide)

All present enzymatic activity of Crystal Structure of Plasmodium Falciparum Dihydroorotate Dehydrogenase Bound with Inhibitor DSM705 (N-(1-(1H-1,2,4-Triazol-3- Yl)Ethyl)-3-Methyl-4-(1-(6-(Trifluoromethyl)Pyridin-3-Yl) Cyclopropyl)-1H-Pyrrole-2-Carboxamide):
1.3.5.2;

Protein crystallography data

The structure of Crystal Structure of Plasmodium Falciparum Dihydroorotate Dehydrogenase Bound with Inhibitor DSM705 (N-(1-(1H-1,2,4-Triazol-3- Yl)Ethyl)-3-Methyl-4-(1-(6-(Trifluoromethyl)Pyridin-3-Yl) Cyclopropyl)-1H-Pyrrole-2-Carboxamide), PDB code: 7kz4 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) 43.65 / 1.75
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 51.914, 157.99, 63.152, 90, 107.01, 90
R / Rfree (%) 17.2 / 20.7

Other elements in 7kz4:

The structure of Crystal Structure of Plasmodium Falciparum Dihydroorotate Dehydrogenase Bound with Inhibitor DSM705 (N-(1-(1H-1,2,4-Triazol-3- Yl)Ethyl)-3-Methyl-4-(1-(6-(Trifluoromethyl)Pyridin-3-Yl) Cyclopropyl)-1H-Pyrrole-2-Carboxamide) also contains other interesting chemical elements:

Magnesium (Mg) 1 atom

Fluorine Binding Sites:

The binding sites of Fluorine atom in the Crystal Structure of Plasmodium Falciparum Dihydroorotate Dehydrogenase Bound with Inhibitor DSM705 (N-(1-(1H-1,2,4-Triazol-3- Yl)Ethyl)-3-Methyl-4-(1-(6-(Trifluoromethyl)Pyridin-3-Yl) Cyclopropyl)-1H-Pyrrole-2-Carboxamide) (pdb code 7kz4). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 6 binding sites of Fluorine where determined in the Crystal Structure of Plasmodium Falciparum Dihydroorotate Dehydrogenase Bound with Inhibitor DSM705 (N-(1-(1H-1,2,4-Triazol-3- Yl)Ethyl)-3-Methyl-4-(1-(6-(Trifluoromethyl)Pyridin-3-Yl) Cyclopropyl)-1H-Pyrrole-2-Carboxamide), PDB code: 7kz4:
Jump to Fluorine binding site number: 1; 2; 3; 4; 5; 6;

Fluorine binding site 1 out of 6 in 7kz4

Go back to Fluorine Binding Sites List in 7kz4
Fluorine binding site 1 out of 6 in the Crystal Structure of Plasmodium Falciparum Dihydroorotate Dehydrogenase Bound with Inhibitor DSM705 (N-(1-(1H-1,2,4-Triazol-3- Yl)Ethyl)-3-Methyl-4-(1-(6-(Trifluoromethyl)Pyridin-3-Yl) Cyclopropyl)-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 DSM705 (N-(1-(1H-1,2,4-Triazol-3- Yl)Ethyl)-3-Methyl-4-(1-(6-(Trifluoromethyl)Pyridin-3-Yl) Cyclopropyl)-1H-Pyrrole-2-Carboxamide) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F1001

b:30.9
occ:1.00
 F25 A:XC71001 0.0 30.9 1.0
C24 A:XC71001 1.4 31.6 1.0
F27 A:XC71001 2.2 31.6 1.0
F26 A:XC71001 2.2 36.3 1.0
H221 A:XC71001 2.3 24.3 1.0
C23 A:XC71001 2.3 17.2 1.0
HD23 A:LEU187 2.4 29.8 0.5
HD21 A:LEU187 2.5 29.8 0.5
C22 A:XC71001 2.7 20.2 1.0
CD2 A:LEU187 2.8 25.2 0.5
HG A:LEU187 3.3 39.6 0.5
N28 A:XC71001 3.6 18.9 1.0
CG A:LEU187 3.6 33.0 0.5
HD22 A:LEU187 3.6 29.8 0.5
SG A:CYS175 3.7 44.0 1.0
HB3 A:LEU187 3.9 32.5 0.5
HB2 A:LEU187 3.9 32.6 0.5
HB3 A:LEU187 3.9 32.6 0.5
HD13 A:LEU187 4.0 36.5 0.5
HG A:CYS175 4.0 52.9 1.0
C21 A:XC71001 4.1 20.2 1.0
HD12 A:LEU187 4.1 36.5 0.5
HD11 A:LEU191 4.2 41.4 1.0
CB A:LEU187 4.3 27.0 0.5
CB A:LEU187 4.4 27.1 0.5
HB3 A:PHE171 4.5 35.0 1.0
CD1 A:LEU187 4.5 30.3 0.5
H211 A:XC71001 4.6 24.3 1.0
C29 A:XC71001 4.6 15.7 1.0
HD11 A:LEU187 4.7 42.5 0.5
HD12 A:LEU191 4.8 41.4 1.0
CD1 A:LEU187 4.8 35.3 0.5
HB2 A:LEU187 4.8 32.5 0.5
HA A:CYS184 4.9 27.7 1.0
C20 A:XC71001 4.9 17.8 1.0
CD1 A:LEU191 4.9 34.5 1.0

Fluorine binding site 2 out of 6 in 7kz4

Go back to Fluorine Binding Sites List in 7kz4
Fluorine binding site 2 out of 6 in the Crystal Structure of Plasmodium Falciparum Dihydroorotate Dehydrogenase Bound with Inhibitor DSM705 (N-(1-(1H-1,2,4-Triazol-3- Yl)Ethyl)-3-Methyl-4-(1-(6-(Trifluoromethyl)Pyridin-3-Yl) Cyclopropyl)-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 DSM705 (N-(1-(1H-1,2,4-Triazol-3- Yl)Ethyl)-3-Methyl-4-(1-(6-(Trifluoromethyl)Pyridin-3-Yl) Cyclopropyl)-1H-Pyrrole-2-Carboxamide) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F1001

b:36.3
occ:1.00
 F26 A:XC71001 0.0 36.3 1.0
C24 A:XC71001 1.4 31.6 1.0
F27 A:XC71001 2.2 31.6 1.0
F25 A:XC71001 2.2 30.9 1.0
C23 A:XC71001 2.4 17.2 1.0
HD11 A:LEU191 2.9 41.4 1.0
N28 A:XC71001 3.0 18.9 1.0
C22 A:XC71001 3.4 20.2 1.0
CD1 A:LEU191 3.5 34.5 1.0
H221 A:XC71001 3.5 24.3 1.0
HD12 A:LEU191 3.5 41.4 1.0
HD13 A:LEU191 3.7 41.4 1.0
HD21 A:LEU187 3.8 29.8 0.5
HG A:LEU187 3.9 39.6 0.5
HE2 A:MET536 4.1 29.7 1.0
C29 A:XC71001 4.2 15.7 1.0
HD23 A:LEU187 4.2 29.8 0.5
O A:HOH1216 4.3 28.8 1.0
HD2 A:PHE171 4.3 57.3 1.0
CD2 A:LEU187 4.4 25.2 0.5
HB3 A:PHE171 4.4 35.0 1.0
HE1 A:MET536 4.4 29.7 1.0
C21 A:XC71001 4.6 20.2 1.0
CG A:LEU187 4.6 33.0 0.5
CE A:MET536 4.6 24.7 1.0
HE3 A:MET536 4.6 29.7 1.0
HB2 A:PHE171 4.8 35.0 1.0
H291 A:XC71001 4.8 19.0 1.0
HD21 A:LEU191 4.9 43.2 1.0
CG A:LEU191 4.9 34.6 1.0
C20 A:XC71001 4.9 17.8 1.0
HB3 A:LEU187 4.9 32.6 0.5
HD1 A:TYR168 4.9 36.0 1.0
CD2 A:PHE171 5.0 47.7 1.0

Fluorine binding site 3 out of 6 in 7kz4

Go back to Fluorine Binding Sites List in 7kz4
Fluorine binding site 3 out of 6 in the Crystal Structure of Plasmodium Falciparum Dihydroorotate Dehydrogenase Bound with Inhibitor DSM705 (N-(1-(1H-1,2,4-Triazol-3- Yl)Ethyl)-3-Methyl-4-(1-(6-(Trifluoromethyl)Pyridin-3-Yl) Cyclopropyl)-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 DSM705 (N-(1-(1H-1,2,4-Triazol-3- Yl)Ethyl)-3-Methyl-4-(1-(6-(Trifluoromethyl)Pyridin-3-Yl) Cyclopropyl)-1H-Pyrrole-2-Carboxamide) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F1001

b:31.6
occ:1.00
 F27 A:XC71001 0.0 31.6 1.0
C24 A:XC71001 1.4 31.6 1.0
F26 A:XC71001 2.2 36.3 1.0
F25 A:XC71001 2.2 30.9 1.0
C23 A:XC71001 2.4 17.2 1.0
HB3 A:PHE171 2.5 35.0 1.0
N28 A:XC71001 2.8 18.9 1.0
HB2 A:PHE171 3.3 35.0 1.0
CB A:PHE171 3.3 29.1 1.0
HG A:CYS175 3.4 52.9 1.0
C22 A:XC71001 3.5 20.2 1.0
SG A:CYS175 3.6 44.0 1.0
O A:HOH1216 3.7 28.8 1.0
H221 A:XC71001 3.8 24.3 1.0
HD2 A:PHE171 3.8 57.3 1.0
C29 A:XC71001 4.1 15.7 1.0
CG A:PHE171 4.2 40.6 1.0
C A:PHE171 4.2 30.6 1.0
O A:PHE171 4.3 28.6 1.0
CD2 A:PHE171 4.3 47.7 1.0
CA A:PHE171 4.4 34.5 1.0
HD21 A:LEU187 4.4 29.8 0.5
HA A:LEU172 4.4 39.4 1.0
HD23 A:LEU187 4.5 29.8 0.5
N A:LEU172 4.6 27.4 1.0
H291 A:XC71001 4.6 19.0 1.0
C21 A:XC71001 4.6 20.2 1.0
HA A:PHE171 4.7 41.4 1.0
HB2 A:CYS175 4.9 37.1 1.0
C20 A:XC71001 4.9 17.8 1.0
H A:LEU172 4.9 32.9 1.0
CD2 A:LEU187 4.9 25.2 0.5
CB A:CYS175 5.0 30.8 1.0

Fluorine binding site 4 out of 6 in 7kz4

Go back to Fluorine Binding Sites List in 7kz4
Fluorine binding site 4 out of 6 in the Crystal Structure of Plasmodium Falciparum Dihydroorotate Dehydrogenase Bound with Inhibitor DSM705 (N-(1-(1H-1,2,4-Triazol-3- Yl)Ethyl)-3-Methyl-4-(1-(6-(Trifluoromethyl)Pyridin-3-Yl) Cyclopropyl)-1H-Pyrrole-2-Carboxamide)


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 DSM705 (N-(1-(1H-1,2,4-Triazol-3- Yl)Ethyl)-3-Methyl-4-(1-(6-(Trifluoromethyl)Pyridin-3-Yl) Cyclopropyl)-1H-Pyrrole-2-Carboxamide) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F1001

b:34.5
occ:1.00
 F25 B:XC71001 0.0 34.5 1.0
C24 B:XC71001 1.4 33.3 1.0
F27 B:XC71001 2.2 26.3 1.0
F26 B:XC71001 2.2 37.1 1.0
C23 B:XC71001 2.4 30.8 1.0
H221 B:XC71001 2.4 30.5 1.0
HD23 B:LEU187 2.5 43.4 1.0
HD21 B:LEU187 2.6 43.4 1.0
C22 B:XC71001 2.7 25.4 1.0
CD2 B:LEU187 2.9 36.1 1.0
HG B:LEU187 3.0 55.5 1.0
CG B:LEU187 3.4 46.2 1.0
HB3 B:LEU187 3.5 33.0 1.0
N28 B:XC71001 3.6 18.3 1.0
SG B:CYS175 3.8 40.3 1.0
HD22 B:LEU187 3.8 43.4 1.0
CB B:LEU187 4.0 27.4 1.0
C21 B:XC71001 4.1 19.7 1.0
HG B:CYS175 4.1 48.5 1.0
HD11 B:LEU191 4.2 46.0 1.0
HB2 B:LEU187 4.5 33.0 1.0
H211 B:XC71001 4.6 23.7 1.0
C29 B:XC71001 4.7 15.7 1.0
HB3 B:PHE171 4.7 35.9 1.0
HA B:CYS184 4.7 28.1 1.0
CD1 B:LEU187 4.7 46.8 1.0
HD12 B:LEU191 4.7 46.0 1.0
HD11 B:LEU187 4.7 56.2 1.0
C20 B:XC71001 4.9 17.5 1.0
CD1 B:LEU191 4.9 38.2 1.0

Fluorine binding site 5 out of 6 in 7kz4

Go back to Fluorine Binding Sites List in 7kz4
Fluorine binding site 5 out of 6 in the Crystal Structure of Plasmodium Falciparum Dihydroorotate Dehydrogenase Bound with Inhibitor DSM705 (N-(1-(1H-1,2,4-Triazol-3- Yl)Ethyl)-3-Methyl-4-(1-(6-(Trifluoromethyl)Pyridin-3-Yl) Cyclopropyl)-1H-Pyrrole-2-Carboxamide)


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 DSM705 (N-(1-(1H-1,2,4-Triazol-3- Yl)Ethyl)-3-Methyl-4-(1-(6-(Trifluoromethyl)Pyridin-3-Yl) Cyclopropyl)-1H-Pyrrole-2-Carboxamide) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F1001

b:37.1
occ:1.00
 F26 B:XC71001 0.0 37.1 1.0
C24 B:XC71001 1.4 33.3 1.0
F27 B:XC71001 2.2 26.3 1.0
F25 B:XC71001 2.2 34.5 1.0
C23 B:XC71001 2.4 30.8 1.0
HD11 B:LEU191 2.6 46.0 1.0
N28 B:XC71001 3.1 18.3 1.0
HD12 B:LEU191 3.2 46.0 1.0
CD1 B:LEU191 3.2 38.2 1.0
C22 B:XC71001 3.2 25.4 1.0
H221 B:XC71001 3.3 30.5 1.0
HG B:LEU187 3.5 55.5 1.0
HD13 B:LEU191 3.6 46.0 1.0
HD21 B:LEU187 4.0 43.4 1.0
HE2 B:MET536 4.2 39.5 1.0
C29 B:XC71001 4.3 15.7 1.0
CG B:LEU187 4.3 46.2 1.0
HD23 B:LEU187 4.3 43.4 1.0
CD2 B:LEU187 4.4 36.1 1.0
C21 B:XC71001 4.5 19.7 1.0
HE1 B:MET536 4.5 39.5 1.0
HE3 B:MET536 4.6 39.5 1.0
CG B:LEU191 4.6 29.1 1.0
HG B:LEU191 4.6 35.0 1.0
CE B:MET536 4.6 32.9 1.0
HB3 B:PHE171 4.7 35.9 1.0
HD21 B:LEU191 4.7 43.1 1.0
HB3 B:LEU187 4.7 33.0 1.0
O B:HOH1227 4.7 21.1 1.0
HD2 B:PHE171 4.7 56.8 1.0
HA B:PHE188 4.8 23.1 1.0
C20 B:XC71001 4.9 17.5 1.0
H291 B:XC71001 4.9 18.9 1.0

Fluorine binding site 6 out of 6 in 7kz4

Go back to Fluorine Binding Sites List in 7kz4
Fluorine binding site 6 out of 6 in the Crystal Structure of Plasmodium Falciparum Dihydroorotate Dehydrogenase Bound with Inhibitor DSM705 (N-(1-(1H-1,2,4-Triazol-3- Yl)Ethyl)-3-Methyl-4-(1-(6-(Trifluoromethyl)Pyridin-3-Yl) Cyclopropyl)-1H-Pyrrole-2-Carboxamide)


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 DSM705 (N-(1-(1H-1,2,4-Triazol-3- Yl)Ethyl)-3-Methyl-4-(1-(6-(Trifluoromethyl)Pyridin-3-Yl) Cyclopropyl)-1H-Pyrrole-2-Carboxamide) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F1001

b:26.3
occ:1.00
 F27 B:XC71001 0.0 26.3 1.0
C24 B:XC71001 1.4 33.3 1.0
F26 B:XC71001 2.2 37.1 1.0
F25 B:XC71001 2.2 34.5 1.0
C23 B:XC71001 2.3 30.8 1.0
N28 B:XC71001 2.7 18.3 1.0
HB3 B:PHE171 2.7 35.9 1.0
C22 B:XC71001 3.5 25.4 1.0
CB B:PHE171 3.5 29.8 1.0
HB2 B:PHE171 3.6 35.9 1.0
HG B:CYS175 3.6 48.5 1.0
SG B:CYS175 3.8 40.3 1.0
H221 B:XC71001 3.8 30.5 1.0
O B:HOH1227 3.9 21.1 1.0
HD2 B:PHE171 3.9 56.8 1.0
C29 B:XC71001 4.0 15.7 1.0
CG B:PHE171 4.3 36.7 1.0
CD2 B:PHE171 4.4 47.2 1.0
C B:PHE171 4.4 29.4 1.0
HD21 B:LEU187 4.5 43.4 1.0
O B:PHE171 4.5 28.7 1.0
H291 B:XC71001 4.5 18.9 1.0
HA B:LEU172 4.6 29.1 1.0
CA B:PHE171 4.6 34.4 1.0
HD23 B:LEU187 4.6 43.4 1.0
C21 B:XC71001 4.7 19.7 1.0
HD11 B:LEU191 4.8 46.0 1.0
N B:LEU172 4.8 26.1 1.0
C20 B:XC71001 4.8 17.5 1.0
HG B:LEU187 4.9 55.5 1.0
HA B:PHE171 5.0 41.4 1.0
CD2 B:LEU187 5.0 36.1 1.0
HE2 B:MET536 5.0 39.5 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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