Atomistry » Fluorine » PDB 7kqj-7l03 » 7l01
Atomistry »
  Fluorine »
    PDB 7kqj-7l03 »
      7l01 »

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

Go back to Fluorine Binding Sites List in 7l01
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: Fri Aug 2 08:39:13 2024

Last articles

Zn in 9JYW
Zn in 9IR4
Zn in 9IR3
Zn in 9GMX
Zn in 9GMW
Zn in 9JEJ
Zn in 9ERF
Zn in 9ERE
Zn in 9EGV
Zn in 9EGW
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy