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: Sat Jul 10 14:11:20 2021

Last articles

Zn in 8WB0
Zn in 8WAX
Zn in 8WAU
Zn in 8WAZ
Zn in 8WAY
Zn in 8WAV
Zn in 8WAW
Zn in 8WAT
Zn in 8W7M
Zn in 8WD3
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy