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

Last articles

Zn in 9MJ5
Zn in 9HNW
Zn in 9G0L
Zn in 9FNE
Zn in 9DZN
Zn in 9E0I
Zn in 9D32
Zn in 9DAK
Zn in 8ZXC
Zn in 8ZUF
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy