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Magnesium 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:

Fluorine (F) 6 atoms

Magnesium Binding Sites:

The binding sites of Magnesium 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 Magnesium atom.
In total only one binding site of Magnesium was 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:

Magnesium binding site 1 out of 1 in 7kz4

Go back to Magnesium Binding Sites List in 7kz4
Magnesium binding site 1 out of 1 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 Magnesium with other atoms in the Mg 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:Mg1004

b:26.9
occ:1.00
 H A:ASP284 2.2 16.6 1.0
OD1 A:ASP284 2.5 24.7 1.0
O A:PRO252 2.6 16.6 1.0
HB2 A:ASP284 2.6 26.9 1.0
O A:HOH1222 2.7 15.1 1.0
HB3 B:LEU447 2.9 20.1 1.0
N A:ASP284 3.0 13.8 1.0
CG A:ASP284 3.2 44.0 1.0
CB A:ASP284 3.2 22.4 1.0
HA3 A:GLY282 3.3 17.4 1.0
H A:CYS283 3.3 16.0 1.0
HD22 B:LEU447 3.3 21.2 1.0
N A:CYS283 3.5 13.3 1.0
HA A:ARG253 3.5 16.4 1.0
HD13 B:LEU447 3.6 22.3 1.0
CA A:ASP284 3.7 16.7 1.0
HH A:TYR327 3.7 23.7 1.0
C A:GLY282 3.7 16.6 1.0
H A:LYS285 3.8 19.2 1.0
CB B:LEU447 3.8 17.1 1.0
C A:PRO252 3.8 10.6 1.0
HB3 A:CYS283 3.9 24.6 1.0
CA A:GLY282 3.9 14.4 1.0
C A:CYS283 4.0 17.0 1.0
HB3 A:ASP284 4.1 26.9 1.0
HE1 A:TYR327 4.2 19.4 1.0
CD2 B:LEU447 4.2 17.6 1.0
HB2 B:LEU447 4.2 20.1 1.0
CA A:CYS283 4.2 10.9 1.0
HA2 A:GLY282 4.3 17.4 1.0
O A:GLY282 4.3 13.0 1.0
OD2 A:ASP284 4.3 54.7 1.0
CG B:LEU447 4.4 16.9 1.0
CA A:ARG253 4.4 13.6 1.0
CD1 B:LEU447 4.4 18.5 1.0
HA A:ASP284 4.4 20.1 1.0
O B:HOH1183 4.4 19.1 1.0
H A:GLY254 4.4 14.9 1.0
N A:LYS285 4.4 16.0 1.0
OH A:TYR327 4.5 19.7 1.0
N A:ARG253 4.6 10.9 1.0
CB A:CYS283 4.6 20.4 1.0
O B:LEU447 4.6 16.4 1.0
C B:LEU447 4.6 16.3 1.0
C A:ASP284 4.6 16.8 1.0
HA A:PRO252 4.7 17.5 1.0
HD23 B:LEU447 4.7 21.2 1.0
HD12 B:LEU447 4.7 22.3 1.0
CA B:LEU447 4.7 15.8 1.0
HD21 B:LEU447 4.8 21.2 1.0
N A:GLY254 4.8 12.3 1.0
HA B:GLU448 4.8 21.2 1.0
O A:MET281 4.8 15.8 1.0
C A:ARG253 4.9 11.5 1.0
CA A:PRO252 4.9 14.5 1.0
HA B:LEU447 4.9 19.1 1.0
CE1 A:TYR327 4.9 16.1 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: Thu Aug 14 08:48:03 2025

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