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Fluorine in PDB 7kzy: Crystal Structure of Plasmodium Falciparum Dihydroorotate Dehydrogenase Bound with Inhibitor DSM778 (3-Methyl-N-(1-(5-Methyl- 1H-Pyrazol-3-Yl)Ethyl)-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 DSM778 (3-Methyl-N-(1-(5-Methyl- 1H-Pyrazol-3-Yl)Ethyl)-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 DSM778 (3-Methyl-N-(1-(5-Methyl- 1H-Pyrazol-3-Yl)Ethyl)-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 DSM778 (3-Methyl-N-(1-(5-Methyl- 1H-Pyrazol-3-Yl)Ethyl)-4-(1-(6-(Trifluoromethyl)Pyridin-3-Yl) Cyclopropyl)-1H-Pyrrole-2-Carboxamide), PDB code: 7kzy 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) 33.03 / 1.75
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 51.409, 158.194, 62.574, 90, 106.24, 90
R / Rfree (%) 16.5 / 20.4

Fluorine Binding Sites:

The binding sites of Fluorine atom in the Crystal Structure of Plasmodium Falciparum Dihydroorotate Dehydrogenase Bound with Inhibitor DSM778 (3-Methyl-N-(1-(5-Methyl- 1H-Pyrazol-3-Yl)Ethyl)-4-(1-(6-(Trifluoromethyl)Pyridin-3-Yl) Cyclopropyl)-1H-Pyrrole-2-Carboxamide) (pdb code 7kzy). 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 DSM778 (3-Methyl-N-(1-(5-Methyl- 1H-Pyrazol-3-Yl)Ethyl)-4-(1-(6-(Trifluoromethyl)Pyridin-3-Yl) Cyclopropyl)-1H-Pyrrole-2-Carboxamide), PDB code: 7kzy:
Jump to Fluorine binding site number: 1; 2; 3; 4; 5; 6;

Fluorine binding site 1 out of 6 in 7kzy

Go back to Fluorine Binding Sites List in 7kzy
Fluorine binding site 1 out of 6 in the Crystal Structure of Plasmodium Falciparum Dihydroorotate Dehydrogenase Bound with Inhibitor DSM778 (3-Methyl-N-(1-(5-Methyl- 1H-Pyrazol-3-Yl)Ethyl)-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 DSM778 (3-Methyl-N-(1-(5-Methyl- 1H-Pyrazol-3-Yl)Ethyl)-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:27.5
occ:1.00
 F26 A:XCM1001 0.0 27.5 1.0
C25 A:XCM1001 1.4 28.2 1.0
F27 A:XCM1001 2.2 29.5 1.0
F28 A:XCM1001 2.2 28.4 1.0
C24 A:XCM1001 2.4 20.8 1.0
HD11 A:LEU191 2.8 41.8 1.0
N29 A:XCM1001 3.0 19.3 1.0
C23 A:XCM1001 3.5 22.0 1.0
CD1 A:LEU191 3.6 34.8 1.0
H231 A:XCM1001 3.7 26.4 1.0
HD12 A:LEU191 3.7 41.8 1.0
HD13 A:LEU191 3.8 41.8 1.0
HB3 A:PHE171 4.0 42.5 1.0
O A:HOH1216 4.2 24.8 1.0
C30 A:XCM1001 4.2 21.4 1.0
HE2 A:MET536 4.2 30.1 1.0
HD2 A:PHE171 4.3 56.1 1.0
HE3 A:MET536 4.3 30.1 1.0
HE1 A:MET536 4.5 30.1 1.0
HB2 A:PHE171 4.6 42.5 1.0
CE A:MET536 4.6 25.0 1.0
C22 A:XCM1001 4.6 21.6 1.0
CB A:PHE171 4.7 35.3 1.0
HD1 A:TYR168 4.7 39.9 1.0
HD21 A:LEU191 4.8 48.7 1.0
H301 A:XCM1001 4.8 25.7 1.0
HB3 A:LEU187 4.8 34.4 1.0
CD2 A:PHE171 4.9 46.7 1.0
CG A:LEU191 4.9 36.3 1.0
C21 A:XCM1001 4.9 23.1 1.0
HD13 A:LEU187 5.0 39.8 1.0

Fluorine binding site 2 out of 6 in 7kzy

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Fluorine binding site 2 out of 6 in the Crystal Structure of Plasmodium Falciparum Dihydroorotate Dehydrogenase Bound with Inhibitor DSM778 (3-Methyl-N-(1-(5-Methyl- 1H-Pyrazol-3-Yl)Ethyl)-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 DSM778 (3-Methyl-N-(1-(5-Methyl- 1H-Pyrazol-3-Yl)Ethyl)-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:29.5
occ:1.00
 F27 A:XCM1001 0.0 29.5 1.0
C25 A:XCM1001 1.4 28.2 1.0
F26 A:XCM1001 2.2 27.5 1.0
F28 A:XCM1001 2.2 28.4 1.0
C24 A:XCM1001 2.3 20.8 1.0
HB3 A:PHE171 2.5 42.5 1.0
N29 A:XCM1001 2.7 19.3 1.0
HG A:CYS175 3.3 49.3 1.0
CB A:PHE171 3.3 35.3 1.0
HB2 A:PHE171 3.4 42.5 1.0
C23 A:XCM1001 3.5 22.0 1.0
SG A:CYS175 3.5 41.1 1.0
H231 A:XCM1001 3.7 26.4 1.0
O A:HOH1216 3.8 24.8 1.0
C30 A:XCM1001 4.0 21.4 1.0
O A:PHE171 4.0 33.3 1.0
C A:PHE171 4.0 32.7 1.0
HD2 A:PHE171 4.2 56.1 1.0
CG A:PHE171 4.2 43.5 1.0
HA A:LEU172 4.3 36.1 1.0
CA A:PHE171 4.3 34.5 1.0
N A:LEU172 4.5 31.8 1.0
H301 A:XCM1001 4.5 25.7 1.0
C22 A:XCM1001 4.6 21.6 1.0
CD2 A:PHE171 4.6 46.7 1.0
HB2 A:CYS175 4.6 44.7 1.0
HA A:PHE171 4.6 41.5 1.0
C21 A:XCM1001 4.8 23.1 1.0
CB A:CYS175 4.8 37.2 1.0
H A:LEU172 4.9 37.8 1.0
CA A:LEU172 4.9 30.4 1.0
HD13 A:LEU187 5.0 39.8 1.0
HD11 A:LEU191 5.0 41.8 1.0

Fluorine binding site 3 out of 6 in 7kzy

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Fluorine binding site 3 out of 6 in the Crystal Structure of Plasmodium Falciparum Dihydroorotate Dehydrogenase Bound with Inhibitor DSM778 (3-Methyl-N-(1-(5-Methyl- 1H-Pyrazol-3-Yl)Ethyl)-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 DSM778 (3-Methyl-N-(1-(5-Methyl- 1H-Pyrazol-3-Yl)Ethyl)-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:28.4
occ:1.00
 F28 A:XCM1001 0.0 28.4 1.0
C25 A:XCM1001 1.3 28.2 1.0
F26 A:XCM1001 2.2 27.5 1.0
F27 A:XCM1001 2.2 29.5 1.0
C24 A:XCM1001 2.3 20.8 1.0
H231 A:XCM1001 2.4 26.4 1.0
C23 A:XCM1001 2.7 22.0 1.0
HD13 A:LEU187 3.0 39.8 1.0
HB3 A:LEU187 3.4 34.4 1.0
N29 A:XCM1001 3.5 19.3 1.0
HD12 A:LEU187 3.7 39.8 1.0
CD1 A:LEU187 3.7 33.1 1.0
HB2 A:LEU187 3.8 34.4 1.0
SG A:CYS175 3.9 41.1 1.0
HD11 A:LEU191 3.9 41.8 1.0
CB A:LEU187 4.0 28.6 1.0
C22 A:XCM1001 4.1 21.6 1.0
HG A:CYS175 4.2 49.3 1.0
HD11 A:LEU187 4.4 39.8 1.0
HB3 A:PHE171 4.5 42.5 1.0
CG A:LEU187 4.5 32.6 1.0
HD12 A:LEU191 4.6 41.8 1.0
C30 A:XCM1001 4.6 21.4 1.0
H221 A:XCM1001 4.7 26.0 1.0
CD1 A:LEU191 4.7 34.8 1.0
HD22 A:LEU187 4.8 45.4 1.0
C21 A:XCM1001 4.9 23.1 1.0

Fluorine binding site 4 out of 6 in 7kzy

Go back to Fluorine Binding Sites List in 7kzy
Fluorine binding site 4 out of 6 in the Crystal Structure of Plasmodium Falciparum Dihydroorotate Dehydrogenase Bound with Inhibitor DSM778 (3-Methyl-N-(1-(5-Methyl- 1H-Pyrazol-3-Yl)Ethyl)-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 DSM778 (3-Methyl-N-(1-(5-Methyl- 1H-Pyrazol-3-Yl)Ethyl)-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:29.5
occ:1.00
 F26 B:XCM1001 0.0 29.5 1.0
C25 B:XCM1001 1.4 27.7 1.0
F28 B:XCM1001 2.2 29.6 1.0
F27 B:XCM1001 2.2 27.2 1.0
C24 B:XCM1001 2.3 20.0 1.0
N29 B:XCM1001 2.8 19.1 1.0
HD11 B:LEU191 2.8 37.8 1.0
C23 B:XCM1001 3.4 22.6 1.0
CD1 B:LEU191 3.4 31.4 1.0
HD12 B:LEU191 3.4 37.8 1.0
HD13 B:LEU191 3.5 37.8 1.0
H231 B:XCM1001 3.6 27.1 1.0
HD2 B:PHE171 4.0 64.3 1.0
C30 B:XCM1001 4.1 20.4 1.0
HE2 B:MET536 4.1 28.1 1.0
O B:HOH1195 4.1 22.9 1.0
HE3 B:MET536 4.2 28.1 1.0
HB3 B:PHE171 4.2 42.0 1.0
HE1 B:MET536 4.4 28.1 1.0
CE B:MET536 4.4 23.4 1.0
C22 B:XCM1001 4.5 22.1 1.0
H301 B:XCM1001 4.6 24.6 1.0
HB3 B:LEU187 4.7 32.4 1.0
C21 B:XCM1001 4.8 20.9 1.0
HD1 B:TYR168 4.8 41.7 1.0
CD2 B:PHE171 4.8 53.5 1.0
CG B:LEU191 4.8 28.1 1.0
HD13 B:LEU187 4.8 43.0 1.0
HD21 B:LEU191 4.9 42.5 1.0
HB2 B:PHE171 4.9 42.0 1.0
CB B:PHE171 5.0 35.0 1.0

Fluorine binding site 5 out of 6 in 7kzy

Go back to Fluorine Binding Sites List in 7kzy
Fluorine binding site 5 out of 6 in the Crystal Structure of Plasmodium Falciparum Dihydroorotate Dehydrogenase Bound with Inhibitor DSM778 (3-Methyl-N-(1-(5-Methyl- 1H-Pyrazol-3-Yl)Ethyl)-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 DSM778 (3-Methyl-N-(1-(5-Methyl- 1H-Pyrazol-3-Yl)Ethyl)-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:27.2
occ:1.00
 F27 B:XCM1001 0.0 27.2 1.0
C25 B:XCM1001 1.3 27.7 1.0
F28 B:XCM1001 2.2 29.6 1.0
F26 B:XCM1001 2.2 29.5 1.0
C24 B:XCM1001 2.3 20.0 1.0
HB3 B:PHE171 2.5 42.0 1.0
N29 B:XCM1001 2.8 19.1 1.0
CB B:PHE171 3.4 35.0 1.0
C23 B:XCM1001 3.4 22.6 1.0
HG B:CYS175 3.5 47.7 1.0
HB2 B:PHE171 3.6 42.0 1.0
H231 B:XCM1001 3.7 27.1 1.0
O B:HOH1195 3.7 22.9 1.0
SG B:CYS175 3.7 39.7 1.0
HD2 B:PHE171 3.7 64.3 1.0
C30 B:XCM1001 4.0 20.4 1.0
C B:PHE171 4.1 35.1 1.0
CG B:PHE171 4.2 41.6 1.0
CD2 B:PHE171 4.2 53.5 1.0
O B:PHE171 4.3 32.5 1.0
HA B:LEU172 4.3 41.0 1.0
CA B:PHE171 4.3 36.2 1.0
N B:LEU172 4.5 30.5 1.0
H301 B:XCM1001 4.5 24.6 1.0
C22 B:XCM1001 4.6 22.1 1.0
HA B:PHE171 4.7 43.5 1.0
C21 B:XCM1001 4.8 20.9 1.0
H B:LEU172 4.8 36.3 1.0
HB2 B:CYS175 4.9 37.7 1.0
CA B:LEU172 4.9 34.1 1.0
HD13 B:LEU187 4.9 43.0 1.0
HD11 B:LEU191 5.0 37.8 1.0

Fluorine binding site 6 out of 6 in 7kzy

Go back to Fluorine Binding Sites List in 7kzy
Fluorine binding site 6 out of 6 in the Crystal Structure of Plasmodium Falciparum Dihydroorotate Dehydrogenase Bound with Inhibitor DSM778 (3-Methyl-N-(1-(5-Methyl- 1H-Pyrazol-3-Yl)Ethyl)-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 DSM778 (3-Methyl-N-(1-(5-Methyl- 1H-Pyrazol-3-Yl)Ethyl)-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:29.6
occ:1.00
 F28 B:XCM1001 0.0 29.6 1.0
C25 B:XCM1001 1.3 27.7 1.0
F26 B:XCM1001 2.2 29.5 1.0
F27 B:XCM1001 2.2 27.2 1.0
C24 B:XCM1001 2.4 20.0 1.0
H231 B:XCM1001 2.4 27.1 1.0
C23 B:XCM1001 2.7 22.6 1.0
HD13 B:LEU187 2.9 43.0 1.0
HB3 B:LEU187 3.4 32.4 1.0
N29 B:XCM1001 3.6 19.1 1.0
CD1 B:LEU187 3.7 35.7 1.0
HD12 B:LEU187 3.8 43.0 1.0
HD11 B:LEU191 3.9 37.8 1.0
SG B:CYS175 4.0 39.7 1.0
HB2 B:LEU187 4.1 32.4 1.0
C22 B:XCM1001 4.1 22.1 1.0
CB B:LEU187 4.2 26.9 1.0
HG B:CYS175 4.3 47.7 1.0
HD11 B:LEU187 4.4 43.0 1.0
HD12 B:LEU191 4.4 37.8 1.0
HB3 B:PHE171 4.5 42.0 1.0
CG B:LEU187 4.6 39.8 1.0
CD1 B:LEU191 4.6 31.4 1.0
C30 B:XCM1001 4.7 20.4 1.0
HD22 B:LEU187 4.7 49.5 1.0
H221 B:XCM1001 4.7 26.6 1.0
C21 B:XCM1001 4.9 20.9 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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