Atomistry » Fluorine » PDB 7ku7-7l4h » 7kzy
Atomistry »
  Fluorine »
    PDB 7ku7-7l4h »
      7kzy »

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

Go back to Fluorine Binding Sites List in 7kzy
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

Go back to Fluorine Binding Sites List in 7kzy
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

Last articles

Zn in 9JPJ
Zn in 9JP7
Zn in 9JPK
Zn in 9JPL
Zn in 9GN6
Zn in 9GN7
Zn in 9GKU
Zn in 9GKW
Zn in 9GKX
Zn in 9GL0
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy