Fluorine in PDB 7l01: Crystal Structure of Plasmodium Falciparum Dihydroorotate Dehydrogenase Bound with Inhibitor DSM782 (N-(1-(5-Cyano-1H-Pyrazol- 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 DSM782 (N-(1-(5-Cyano-1H-Pyrazol- 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 DSM782 (N-(1-(5-Cyano-1H-Pyrazol- 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 DSM782 (N-(1-(5-Cyano-1H-Pyrazol- 3-Yl)Ethyl)-3-Methyl-4-(1-(6-(Trifluoromethyl)Pyridin-3-Yl) Cyclopropyl)-1H-Pyrrole-2-Carboxamide), PDB code: 7l01 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) 33.39 / 1.60
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 50.059, 158.027, 61.05, 90, 104.6, 90
R / Rfree (%) 16.4 / 18.8

Fluorine Binding Sites:

The binding sites of Fluorine atom in the Crystal Structure of Plasmodium Falciparum Dihydroorotate Dehydrogenase Bound with Inhibitor DSM782 (N-(1-(5-Cyano-1H-Pyrazol- 3-Yl)Ethyl)-3-Methyl-4-(1-(6-(Trifluoromethyl)Pyridin-3-Yl) Cyclopropyl)-1H-Pyrrole-2-Carboxamide) (pdb code 7l01). 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 DSM782 (N-(1-(5-Cyano-1H-Pyrazol- 3-Yl)Ethyl)-3-Methyl-4-(1-(6-(Trifluoromethyl)Pyridin-3-Yl) Cyclopropyl)-1H-Pyrrole-2-Carboxamide), PDB code: 7l01:
Jump to Fluorine binding site number: 1; 2; 3; 4; 5; 6;

Fluorine binding site 1 out of 6 in 7l01

Go back to Fluorine Binding Sites List in 7l01
Fluorine binding site 1 out of 6 in the Crystal Structure of Plasmodium Falciparum Dihydroorotate Dehydrogenase Bound with Inhibitor DSM782 (N-(1-(5-Cyano-1H-Pyrazol- 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 DSM782 (N-(1-(5-Cyano-1H-Pyrazol- 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:24.6
occ:1.00
 F27 A:XCV1001 0.0 24.6 1.0
C26 A:XCV1001 1.4 21.2 1.0
F29 A:XCV1001 2.2 23.4 1.0
F28 A:XCV1001 2.2 25.5 1.0
H241 A:XCV1001 2.4 21.5 1.0
C25 A:XCV1001 2.4 15.2 1.0
C24 A:XCV1001 2.7 17.9 1.0
HD13 A:LEU187 2.7 28.0 1.0
HB3 A:LEU187 3.3 22.3 1.0
HD12 A:LEU187 3.4 28.0 1.0
CD1 A:LEU187 3.5 23.3 1.0
N30 A:XCV1001 3.6 19.2 1.0
HB2 A:LEU187 3.7 22.3 1.0
HD11 A:LEU191 3.9 29.9 1.0
CB A:LEU187 3.9 18.5 1.0
SG A:CYS175 3.9 30.5 1.0
C23 A:XCV1001 4.1 16.2 1.0
HD11 A:LEU187 4.2 28.0 1.0
HG A:CYS175 4.3 36.6 1.0
CG A:LEU187 4.3 24.5 1.0
HD12 A:LEU191 4.5 29.9 1.0
HD22 A:LEU187 4.6 33.5 1.0
CD1 A:LEU191 4.6 24.8 1.0
H231 A:XCV1001 4.6 19.5 1.0
HB3 A:PHE171 4.6 33.5 1.0
C31 A:XCV1001 4.7 16.5 1.0
C22 A:XCV1001 4.9 17.1 1.0
HA A:CYS184 4.9 19.9 1.0

Fluorine binding site 2 out of 6 in 7l01

Go back to Fluorine Binding Sites List in 7l01
Fluorine binding site 2 out of 6 in the Crystal Structure of Plasmodium Falciparum Dihydroorotate Dehydrogenase Bound with Inhibitor DSM782 (N-(1-(5-Cyano-1H-Pyrazol- 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 DSM782 (N-(1-(5-Cyano-1H-Pyrazol- 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:25.5
occ:1.00
 F28 A:XCV1001 0.0 25.5 1.0
C26 A:XCV1001 1.4 21.2 1.0
F29 A:XCV1001 2.2 23.4 1.0
F27 A:XCV1001 2.2 24.6 1.0
C25 A:XCV1001 2.4 15.2 1.0
HD11 A:LEU191 2.8 29.9 1.0
N30 A:XCV1001 2.9 19.2 1.0
C24 A:XCV1001 3.4 17.9 1.0
CD1 A:LEU191 3.5 24.8 1.0
HD12 A:LEU191 3.6 29.9 1.0
HD13 A:LEU191 3.6 29.9 1.0
H241 A:XCV1001 3.6 21.5 1.0
HD2 A:PHE171 4.1 49.1 1.0
O A:HOH1239 4.1 19.6 1.0
HE2 A:MET536 4.1 24.6 1.0
C31 A:XCV1001 4.1 16.5 1.0
HB3 A:PHE171 4.3 33.5 1.0
HE3 A:MET536 4.3 24.6 1.0
HE1 A:MET536 4.4 24.6 1.0
CE A:MET536 4.4 20.5 1.0
C23 A:XCV1001 4.6 16.2 1.0
HB3 A:LEU187 4.6 22.3 1.0
HD21 A:LEU191 4.7 34.8 1.0
H311 A:XCV1001 4.7 19.8 1.0
HB2 A:PHE171 4.7 33.5 1.0
HD13 A:LEU187 4.8 28.0 1.0
HD1 A:TYR168 4.8 31.4 1.0
CG A:LEU191 4.8 22.4 1.0
C22 A:XCV1001 4.9 17.1 1.0
CD2 A:PHE171 4.9 40.9 1.0
CB A:PHE171 4.9 27.9 1.0

Fluorine binding site 3 out of 6 in 7l01

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Fluorine binding site 3 out of 6 in the Crystal Structure of Plasmodium Falciparum Dihydroorotate Dehydrogenase Bound with Inhibitor DSM782 (N-(1-(5-Cyano-1H-Pyrazol- 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 DSM782 (N-(1-(5-Cyano-1H-Pyrazol- 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:23.4
occ:1.00
 F29 A:XCV1001 0.0 23.4 1.0
C26 A:XCV1001 1.3 21.2 1.0
F27 A:XCV1001 2.2 24.6 1.0
F28 A:XCV1001 2.2 25.5 1.0
C25 A:XCV1001 2.3 15.2 1.0
HB3 A:PHE171 2.6 33.5 1.0
N30 A:XCV1001 2.8 19.2 1.0
HG A:CYS175 3.3 36.6 1.0
C24 A:XCV1001 3.4 17.9 1.0
CB A:PHE171 3.5 27.9 1.0
SG A:CYS175 3.5 30.5 1.0
HB2 A:PHE171 3.5 33.5 1.0
H241 A:XCV1001 3.6 21.5 1.0
O A:HOH1239 3.8 19.6 1.0
HD2 A:PHE171 3.9 49.1 1.0
C31 A:XCV1001 4.1 16.5 1.0
O A:PHE171 4.1 24.8 1.0
C A:PHE171 4.2 26.9 1.0
HA A:LEU172 4.3 28.1 1.0
CG A:PHE171 4.4 34.5 1.0
CA A:PHE171 4.4 24.3 1.0
CD2 A:PHE171 4.4 40.9 1.0
C23 A:XCV1001 4.6 16.2 1.0
N A:LEU172 4.6 22.6 1.0
H311 A:XCV1001 4.6 19.8 1.0
HD13 A:LEU187 4.7 28.0 1.0
HB2 A:CYS175 4.8 27.5 1.0
HA A:PHE171 4.8 29.3 1.0
C22 A:XCV1001 4.8 17.1 1.0
CB A:CYS175 4.9 22.8 1.0
HD11 A:LEU191 4.9 29.9 1.0
H A:LEU172 4.9 27.2 1.0
CA A:LEU172 5.0 23.4 1.0

Fluorine binding site 4 out of 6 in 7l01

Go back to Fluorine Binding Sites List in 7l01
Fluorine binding site 4 out of 6 in the Crystal Structure of Plasmodium Falciparum Dihydroorotate Dehydrogenase Bound with Inhibitor DSM782 (N-(1-(5-Cyano-1H-Pyrazol- 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 DSM782 (N-(1-(5-Cyano-1H-Pyrazol- 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:24.4
occ:1.00
 F27 B:XCV1001 0.0 24.4 1.0
C26 B:XCV1001 1.4 19.4 1.0
F28 B:XCV1001 2.2 24.7 1.0
F29 B:XCV1001 2.2 25.3 1.0
H241 B:XCV1001 2.3 23.1 1.0
C25 B:XCV1001 2.3 18.8 1.0
C24 B:XCV1001 2.6 19.2 1.0
HD13 B:LEU187 3.0 37.3 1.0
HB3 B:LEU187 3.3 28.8 1.0
N30 B:XCV1001 3.6 22.8 1.0
HD12 B:LEU187 3.8 37.3 1.0
CD1 B:LEU187 3.8 31.1 1.0
HB2 B:LEU187 3.9 28.8 1.0
SG B:CYS175 3.9 32.0 1.0
CB B:LEU187 4.0 23.9 1.0
HD11 B:LEU191 4.0 29.0 1.0
C23 B:XCV1001 4.0 17.0 1.0
HG B:CYS175 4.2 38.5 1.0
CG B:LEU187 4.5 27.6 1.0
HB3 B:PHE171 4.5 35.8 1.0
HD11 B:LEU187 4.6 37.3 1.0
H231 B:XCV1001 4.6 20.5 1.0
C31 B:XCV1001 4.6 19.9 1.0
HD12 B:LEU191 4.7 29.0 1.0
HD22 B:LEU187 4.8 34.9 1.0
CD1 B:LEU191 4.8 24.1 1.0
C22 B:XCV1001 4.9 18.4 1.0
HA B:CYS184 5.0 25.4 1.0

Fluorine binding site 5 out of 6 in 7l01

Go back to Fluorine Binding Sites List in 7l01
Fluorine binding site 5 out of 6 in the Crystal Structure of Plasmodium Falciparum Dihydroorotate Dehydrogenase Bound with Inhibitor DSM782 (N-(1-(5-Cyano-1H-Pyrazol- 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 DSM782 (N-(1-(5-Cyano-1H-Pyrazol- 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:24.7
occ:1.00
 F28 B:XCV1001 0.0 24.7 1.0
C26 B:XCV1001 1.4 19.4 1.0
F27 B:XCV1001 2.2 24.4 1.0
F29 B:XCV1001 2.2 25.3 1.0
C25 B:XCV1001 2.4 18.8 1.0
HD11 B:LEU191 2.8 29.0 1.0
N30 B:XCV1001 2.9 22.8 1.0
C24 B:XCV1001 3.4 19.2 1.0
CD1 B:LEU191 3.5 24.1 1.0
H241 B:XCV1001 3.6 23.1 1.0
HD12 B:LEU191 3.6 29.0 1.0
HD13 B:LEU191 3.7 29.0 1.0
HE2 B:MET536 4.1 23.6 1.0
O B:HOH1219 4.1 20.2 1.0
C31 B:XCV1001 4.1 19.9 1.0
HE3 B:MET536 4.2 23.6 1.0
HD2 B:PHE171 4.2 45.7 1.0
HB3 B:PHE171 4.3 35.8 1.0
HE1 B:MET536 4.4 23.6 1.0
CE B:MET536 4.4 19.6 1.0
C23 B:XCV1001 4.6 17.0 1.0
HB3 B:LEU187 4.6 28.8 1.0
HB2 B:PHE171 4.7 35.8 1.0
H311 B:XCV1001 4.7 23.9 1.0
HD1 B:TYR168 4.8 28.1 1.0
HD21 B:LEU191 4.8 38.6 1.0
C22 B:XCV1001 4.9 18.4 1.0
CG B:LEU191 4.9 24.4 1.0
CB B:PHE171 4.9 29.7 1.0
CD2 B:PHE171 5.0 38.0 1.0

Fluorine binding site 6 out of 6 in 7l01

Go back to Fluorine Binding Sites List in 7l01
Fluorine binding site 6 out of 6 in the Crystal Structure of Plasmodium Falciparum Dihydroorotate Dehydrogenase Bound with Inhibitor DSM782 (N-(1-(5-Cyano-1H-Pyrazol- 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 DSM782 (N-(1-(5-Cyano-1H-Pyrazol- 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:25.3
occ:1.00
 F29 B:XCV1001 0.0 25.3 1.0
C26 B:XCV1001 1.3 19.4 1.0
F28 B:XCV1001 2.2 24.7 1.0
F27 B:XCV1001 2.2 24.4 1.0
C25 B:XCV1001 2.3 18.8 1.0
HB3 B:PHE171 2.5 35.8 1.0
N30 B:XCV1001 2.8 22.8 1.0
HG B:CYS175 3.3 38.5 1.0
CB B:PHE171 3.3 29.7 1.0
HB2 B:PHE171 3.3 35.8 1.0
C24 B:XCV1001 3.5 19.2 1.0
SG B:CYS175 3.6 32.0 1.0
H241 B:XCV1001 3.7 23.1 1.0
O B:HOH1219 3.7 20.2 1.0
HD2 B:PHE171 3.9 45.7 1.0
C31 B:XCV1001 4.1 19.9 1.0
C B:PHE171 4.1 26.7 1.0
CG B:PHE171 4.2 34.4 1.0
O B:PHE171 4.2 25.5 1.0
CA B:PHE171 4.3 24.5 1.0
HA B:LEU172 4.4 31.0 1.0
CD2 B:PHE171 4.4 38.0 1.0
N B:LEU172 4.5 28.5 1.0
C23 B:XCV1001 4.6 17.0 1.0
HA B:PHE171 4.7 29.0 1.0
H311 B:XCV1001 4.7 23.9 1.0
H B:LEU172 4.8 34.3 1.0
HB2 B:CYS175 4.8 34.4 1.0
C22 B:XCV1001 4.9 18.4 1.0
CA B:LEU172 5.0 25.8 1.0
CB B:CYS175 5.0 28.6 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: Sat Jul 10 14:11:21 2021

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