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Fluorine in PDB 6oex: Crystal Structure of Trypanothione Reductase From Trypanosoma Brucei in Complex with Inhibitor 3-(2-{1-[2-(Piperidin-4-Yl)Ethyl]-1H-Indol- 5-Yl}-5-[1-(Pyrrolidin-1-Yl)Cyclohexyl]-1,3- Thiazol-4-Yl)-N-(2,2,2- Trifluoroethyl)Prop-2-Yn-1-Amine

Enzymatic activity of Crystal Structure of Trypanothione Reductase From Trypanosoma Brucei in Complex with Inhibitor 3-(2-{1-[2-(Piperidin-4-Yl)Ethyl]-1H-Indol- 5-Yl}-5-[1-(Pyrrolidin-1-Yl)Cyclohexyl]-1,3- Thiazol-4-Yl)-N-(2,2,2- Trifluoroethyl)Prop-2-Yn-1-Amine

All present enzymatic activity of Crystal Structure of Trypanothione Reductase From Trypanosoma Brucei in Complex with Inhibitor 3-(2-{1-[2-(Piperidin-4-Yl)Ethyl]-1H-Indol- 5-Yl}-5-[1-(Pyrrolidin-1-Yl)Cyclohexyl]-1,3- Thiazol-4-Yl)-N-(2,2,2- Trifluoroethyl)Prop-2-Yn-1-Amine:
1.8.1.12;

Protein crystallography data

The structure of Crystal Structure of Trypanothione Reductase From Trypanosoma Brucei in Complex with Inhibitor 3-(2-{1-[2-(Piperidin-4-Yl)Ethyl]-1H-Indol- 5-Yl}-5-[1-(Pyrrolidin-1-Yl)Cyclohexyl]-1,3- Thiazol-4-Yl)-N-(2,2,2- Trifluoroethyl)Prop-2-Yn-1-Amine, PDB code: 6oex was solved by O.Halgas, R.De Gasparo, D.Harangozo, R.L.Krauth-Siegel, F.Diederich, E.F.Pai, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 46.40 / 2.10
Space group P 43 21 2
Cell size a, b, c (Å), α, β, γ (°) 117.190, 117.190, 224.170, 90.00, 90.00, 90.00
R / Rfree (%) 17.6 / 19.2

Fluorine Binding Sites:

The binding sites of Fluorine atom in the Crystal Structure of Trypanothione Reductase From Trypanosoma Brucei in Complex with Inhibitor 3-(2-{1-[2-(Piperidin-4-Yl)Ethyl]-1H-Indol- 5-Yl}-5-[1-(Pyrrolidin-1-Yl)Cyclohexyl]-1,3- Thiazol-4-Yl)-N-(2,2,2- Trifluoroethyl)Prop-2-Yn-1-Amine (pdb code 6oex). 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 Trypanothione Reductase From Trypanosoma Brucei in Complex with Inhibitor 3-(2-{1-[2-(Piperidin-4-Yl)Ethyl]-1H-Indol- 5-Yl}-5-[1-(Pyrrolidin-1-Yl)Cyclohexyl]-1,3- Thiazol-4-Yl)-N-(2,2,2- Trifluoroethyl)Prop-2-Yn-1-Amine, PDB code: 6oex:
Jump to Fluorine binding site number: 1; 2; 3; 4; 5; 6;

Fluorine binding site 1 out of 6 in 6oex

Go back to Fluorine Binding Sites List in 6oex
Fluorine binding site 1 out of 6 in the Crystal Structure of Trypanothione Reductase From Trypanosoma Brucei in Complex with Inhibitor 3-(2-{1-[2-(Piperidin-4-Yl)Ethyl]-1H-Indol- 5-Yl}-5-[1-(Pyrrolidin-1-Yl)Cyclohexyl]-1,3- Thiazol-4-Yl)-N-(2,2,2- Trifluoroethyl)Prop-2-Yn-1-Amine


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 Trypanothione Reductase From Trypanosoma Brucei in Complex with Inhibitor 3-(2-{1-[2-(Piperidin-4-Yl)Ethyl]-1H-Indol- 5-Yl}-5-[1-(Pyrrolidin-1-Yl)Cyclohexyl]-1,3- Thiazol-4-Yl)-N-(2,2,2- Trifluoroethyl)Prop-2-Yn-1-Amine within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F505

b:84.8
occ:1.00
 F2 B:M9Y505 0.0 84.8 1.0
C B:M9Y505 1.3 83.2 1.0
F B:M9Y505 2.1 83.8 1.0
F1 B:M9Y505 2.1 83.8 1.0
C1 B:M9Y505 2.3 79.9 1.0
N B:M9Y505 2.8 75.5 1.0
C2 B:M9Y505 3.5 72.4 1.0
CG2 B:VAL53 3.9 35.0 1.0
OH B:TYR110 4.0 53.1 1.0
CG2 B:VAL58 4.2 36.8 1.0
CD1 B:ILE106 4.3 34.7 1.0
CG2 B:ILE106 4.6 34.5 1.0
CE1 A:HIS461 4.6 42.6 1.0
NE2 A:HIS461 4.7 38.5 1.0
C3 B:M9Y505 4.8 70.5 1.0

Fluorine binding site 2 out of 6 in 6oex

Go back to Fluorine Binding Sites List in 6oex
Fluorine binding site 2 out of 6 in the Crystal Structure of Trypanothione Reductase From Trypanosoma Brucei in Complex with Inhibitor 3-(2-{1-[2-(Piperidin-4-Yl)Ethyl]-1H-Indol- 5-Yl}-5-[1-(Pyrrolidin-1-Yl)Cyclohexyl]-1,3- Thiazol-4-Yl)-N-(2,2,2- Trifluoroethyl)Prop-2-Yn-1-Amine


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 Trypanothione Reductase From Trypanosoma Brucei in Complex with Inhibitor 3-(2-{1-[2-(Piperidin-4-Yl)Ethyl]-1H-Indol- 5-Yl}-5-[1-(Pyrrolidin-1-Yl)Cyclohexyl]-1,3- Thiazol-4-Yl)-N-(2,2,2- Trifluoroethyl)Prop-2-Yn-1-Amine within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F505

b:83.8
occ:1.00
 F B:M9Y505 0.0 83.8 1.0
C B:M9Y505 1.3 83.2 1.0
F1 B:M9Y505 2.0 83.8 1.0
F2 B:M9Y505 2.1 84.8 1.0
C1 B:M9Y505 2.3 79.9 1.0
C2 B:M9Y505 2.9 72.4 1.0
N B:M9Y505 2.9 75.5 1.0
C2 A:EPE502 3.9 79.1 1.0
CE1 A:HIS461 4.2 42.6 1.0
C3 B:M9Y505 4.3 70.5 1.0
N1 A:EPE502 4.5 77.0 1.0
C7 A:EPE502 4.8 85.1 1.0
C3 A:EPE502 4.8 80.7 1.0
NE2 A:HIS461 4.9 38.5 1.0
N4 A:EPE502 4.9 82.6 1.0
C5 A:EPE502 5.0 80.7 1.0

Fluorine binding site 3 out of 6 in 6oex

Go back to Fluorine Binding Sites List in 6oex
Fluorine binding site 3 out of 6 in the Crystal Structure of Trypanothione Reductase From Trypanosoma Brucei in Complex with Inhibitor 3-(2-{1-[2-(Piperidin-4-Yl)Ethyl]-1H-Indol- 5-Yl}-5-[1-(Pyrrolidin-1-Yl)Cyclohexyl]-1,3- Thiazol-4-Yl)-N-(2,2,2- Trifluoroethyl)Prop-2-Yn-1-Amine


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 Trypanothione Reductase From Trypanosoma Brucei in Complex with Inhibitor 3-(2-{1-[2-(Piperidin-4-Yl)Ethyl]-1H-Indol- 5-Yl}-5-[1-(Pyrrolidin-1-Yl)Cyclohexyl]-1,3- Thiazol-4-Yl)-N-(2,2,2- Trifluoroethyl)Prop-2-Yn-1-Amine within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F505

b:83.8
occ:1.00
 F1 B:M9Y505 0.0 83.8 1.0
C B:M9Y505 1.3 83.2 1.0
F B:M9Y505 2.0 83.8 1.0
F2 B:M9Y505 2.1 84.8 1.0
C1 B:M9Y505 2.3 79.9 1.0
CD2 A:LEU399 3.5 53.1 1.0
N B:M9Y505 3.6 75.5 1.0
CD1 B:ILE106 3.8 34.7 1.0
CG2 B:VAL58 4.1 36.8 1.0
C2 B:M9Y505 4.2 72.4 1.0
CG A:LEU399 4.6 51.6 1.0
CG1 B:ILE106 4.7 33.0 1.0
CD1 A:LEU399 4.7 52.1 1.0
C2 A:EPE502 4.8 79.1 1.0
CE1 A:HIS461 4.8 42.6 1.0

Fluorine binding site 4 out of 6 in 6oex

Go back to Fluorine Binding Sites List in 6oex
Fluorine binding site 4 out of 6 in the Crystal Structure of Trypanothione Reductase From Trypanosoma Brucei in Complex with Inhibitor 3-(2-{1-[2-(Piperidin-4-Yl)Ethyl]-1H-Indol- 5-Yl}-5-[1-(Pyrrolidin-1-Yl)Cyclohexyl]-1,3- Thiazol-4-Yl)-N-(2,2,2- Trifluoroethyl)Prop-2-Yn-1-Amine


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 Trypanothione Reductase From Trypanosoma Brucei in Complex with Inhibitor 3-(2-{1-[2-(Piperidin-4-Yl)Ethyl]-1H-Indol- 5-Yl}-5-[1-(Pyrrolidin-1-Yl)Cyclohexyl]-1,3- Thiazol-4-Yl)-N-(2,2,2- Trifluoroethyl)Prop-2-Yn-1-Amine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F503

b:0.1
occ:1.00
 F2 A:M9Y503 0.0 0.1 1.0
C A:M9Y503 1.3 0.7 1.0
F1 A:M9Y503 2.1 0.4 1.0
F A:M9Y503 2.1 0.3 1.0
C1 A:M9Y503 2.3 0.4 1.0
N A:M9Y503 2.9 0.5 1.0
CD1 A:ILE106 3.8 44.9 1.0
C2 A:M9Y503 3.9 0.3 1.0
O A:HOH874 4.4 61.2 1.0
CG1 A:ILE106 4.4 45.3 1.0
CG2 A:VAL58 4.5 44.9 1.0
CG2 A:ILE106 4.7 44.9 1.0

Fluorine binding site 5 out of 6 in 6oex

Go back to Fluorine Binding Sites List in 6oex
Fluorine binding site 5 out of 6 in the Crystal Structure of Trypanothione Reductase From Trypanosoma Brucei in Complex with Inhibitor 3-(2-{1-[2-(Piperidin-4-Yl)Ethyl]-1H-Indol- 5-Yl}-5-[1-(Pyrrolidin-1-Yl)Cyclohexyl]-1,3- Thiazol-4-Yl)-N-(2,2,2- Trifluoroethyl)Prop-2-Yn-1-Amine


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 Trypanothione Reductase From Trypanosoma Brucei in Complex with Inhibitor 3-(2-{1-[2-(Piperidin-4-Yl)Ethyl]-1H-Indol- 5-Yl}-5-[1-(Pyrrolidin-1-Yl)Cyclohexyl]-1,3- Thiazol-4-Yl)-N-(2,2,2- Trifluoroethyl)Prop-2-Yn-1-Amine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F503

b:0.3
occ:1.00
 F A:M9Y503 0.0 0.3 1.0
C A:M9Y503 1.3 0.7 1.0
F1 A:M9Y503 2.1 0.4 1.0
F2 A:M9Y503 2.1 0.1 1.0
C1 A:M9Y503 2.3 0.4 1.0
N A:M9Y503 3.6 0.5 1.0
CG2 A:VAL58 3.6 44.9 1.0
CG2 A:VAL53 4.0 44.6 1.0
C2 A:M9Y503 4.2 0.3 1.0
NE2 B:HIS461 4.2 42.2 1.0
CE1 B:HIS461 4.3 44.4 1.0
CD1 A:ILE106 4.7 44.9 1.0
OH A:TYR110 4.9 59.6 1.0
CB A:VAL58 5.0 42.1 1.0

Fluorine binding site 6 out of 6 in 6oex

Go back to Fluorine Binding Sites List in 6oex
Fluorine binding site 6 out of 6 in the Crystal Structure of Trypanothione Reductase From Trypanosoma Brucei in Complex with Inhibitor 3-(2-{1-[2-(Piperidin-4-Yl)Ethyl]-1H-Indol- 5-Yl}-5-[1-(Pyrrolidin-1-Yl)Cyclohexyl]-1,3- Thiazol-4-Yl)-N-(2,2,2- Trifluoroethyl)Prop-2-Yn-1-Amine


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 Trypanothione Reductase From Trypanosoma Brucei in Complex with Inhibitor 3-(2-{1-[2-(Piperidin-4-Yl)Ethyl]-1H-Indol- 5-Yl}-5-[1-(Pyrrolidin-1-Yl)Cyclohexyl]-1,3- Thiazol-4-Yl)-N-(2,2,2- Trifluoroethyl)Prop-2-Yn-1-Amine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F503

b:0.4
occ:1.00
 F1 A:M9Y503 0.0 0.4 1.0
C A:M9Y503 1.3 0.7 1.0
F A:M9Y503 2.1 0.3 1.0
F2 A:M9Y503 2.1 0.1 1.0
C1 A:M9Y503 2.3 0.4 1.0
N A:M9Y503 2.7 0.5 1.0
C2 A:M9Y503 2.9 0.3 1.0
C3 A:M9Y503 4.4 99.8 1.0
CE1 B:HIS461 4.4 44.4 1.0
NE2 B:HIS461 4.9 42.2 1.0

Reference:

R.De Gasparo, O.Halgas, D.Harangozo, M.Kaiser, E.F.Pai, R.L.Krauth-Siegel, F.Diederich. Targeting A Large Active Site: Structure-Based Design of Nanomolar Inhibitors of Trypanosoma Brucei Trypanothione Reductase. Chemistry V. 25 11416 2019.
ISSN: ISSN 0947-6539
PubMed: 31407832
DOI: 10.1002/CHEM.201901664
Page generated: Thu Aug 1 23:35:24 2024

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