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Fluorine in PDB 4uqh: Crystal Structure of Trypanosoma Cruzi CYP51 Bound to the Inhibitor (R)-N-(3-(1H-Indol-3-Yl)-1-Oxo-1-(Pyridin-4- Ylamino)Propan-2-Yl)-4-(4-(3,4-Difluorophenyl)Piperazin-1- Yl)-2-Fluorobenzamide.

Enzymatic activity of Crystal Structure of Trypanosoma Cruzi CYP51 Bound to the Inhibitor (R)-N-(3-(1H-Indol-3-Yl)-1-Oxo-1-(Pyridin-4- Ylamino)Propan-2-Yl)-4-(4-(3,4-Difluorophenyl)Piperazin-1- Yl)-2-Fluorobenzamide.

All present enzymatic activity of Crystal Structure of Trypanosoma Cruzi CYP51 Bound to the Inhibitor (R)-N-(3-(1H-Indol-3-Yl)-1-Oxo-1-(Pyridin-4- Ylamino)Propan-2-Yl)-4-(4-(3,4-Difluorophenyl)Piperazin-1- Yl)-2-Fluorobenzamide.:
1.14.13.70;

Protein crystallography data

The structure of Crystal Structure of Trypanosoma Cruzi CYP51 Bound to the Inhibitor (R)-N-(3-(1H-Indol-3-Yl)-1-Oxo-1-(Pyridin-4- Ylamino)Propan-2-Yl)-4-(4-(3,4-Difluorophenyl)Piperazin-1- Yl)-2-Fluorobenzamide., PDB code: 4uqh was solved by C.M.Calvet, D.F.Vieira, J.Y.Choi, M.D.Cameron, J.Gut, D.Kellar, J.L.Siqueira-Neto, J.H.Mckerrow, W.R.Roush, L.M.Podust, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 111.19 / 2.43
Space group P 63 2 2
Cell size a, b, c (Å), α, β, γ (°) 128.394, 128.394, 116.573, 90.00, 90.00, 120.00
R / Rfree (%) 19.44 / 24.651

Other elements in 4uqh:

The structure of Crystal Structure of Trypanosoma Cruzi CYP51 Bound to the Inhibitor (R)-N-(3-(1H-Indol-3-Yl)-1-Oxo-1-(Pyridin-4- Ylamino)Propan-2-Yl)-4-(4-(3,4-Difluorophenyl)Piperazin-1- Yl)-2-Fluorobenzamide. also contains other interesting chemical elements:

Iron (Fe) 1 atom

Fluorine Binding Sites:

The binding sites of Fluorine atom in the Crystal Structure of Trypanosoma Cruzi CYP51 Bound to the Inhibitor (R)-N-(3-(1H-Indol-3-Yl)-1-Oxo-1-(Pyridin-4- Ylamino)Propan-2-Yl)-4-(4-(3,4-Difluorophenyl)Piperazin-1- Yl)-2-Fluorobenzamide. (pdb code 4uqh). 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 Trypanosoma Cruzi CYP51 Bound to the Inhibitor (R)-N-(3-(1H-Indol-3-Yl)-1-Oxo-1-(Pyridin-4- Ylamino)Propan-2-Yl)-4-(4-(3,4-Difluorophenyl)Piperazin-1- Yl)-2-Fluorobenzamide., PDB code: 4uqh:
Jump to Fluorine binding site number: 1; 2; 3;

Fluorine binding site 1 out of 3 in 4uqh

Go back to Fluorine Binding Sites List in 4uqh
Fluorine binding site 1 out of 3 in the Crystal Structure of Trypanosoma Cruzi CYP51 Bound to the Inhibitor (R)-N-(3-(1H-Indol-3-Yl)-1-Oxo-1-(Pyridin-4- Ylamino)Propan-2-Yl)-4-(4-(3,4-Difluorophenyl)Piperazin-1- Yl)-2-Fluorobenzamide.


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 Trypanosoma Cruzi CYP51 Bound to the Inhibitor (R)-N-(3-(1H-Indol-3-Yl)-1-Oxo-1-(Pyridin-4- Ylamino)Propan-2-Yl)-4-(4-(3,4-Difluorophenyl)Piperazin-1- Yl)-2-Fluorobenzamide. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F1485

b:36.0
occ:1.00
 F2 A:25S1485 0.0 36.0 1.0
C23 A:25S1485 1.3 32.3 1.0
C22 A:25S1485 2.3 34.3 1.0
C8 A:25S1485 2.4 32.2 1.0
N2 A:25S1485 2.8 34.3 1.0
C7 A:25S1485 3.0 33.0 1.0
C11 A:25S1485 3.6 37.4 1.0
C9 A:25S1485 3.7 34.9 1.0
CE1 A:TYR103 3.7 77.7 1.0
C26 A:25S1485 3.8 47.3 1.0
CD1 A:ILE105 3.8 37.9 1.0
CD1 A:TYR103 4.0 74.9 1.0
O A:HOH2014 4.0 50.7 1.0
C10 A:25S1485 4.1 36.1 1.0
C6 A:25S1485 4.2 34.1 1.0
O A:25S1485 4.2 39.1 1.0
C24 A:25S1485 4.4 38.4 1.0
C25 A:25S1485 4.5 43.4 1.0
N3 A:25S1485 4.7 42.1 1.0
CG1 A:ILE105 4.8 37.2 1.0
CZ A:TYR103 4.8 77.5 1.0
SD A:MET460 4.8 53.2 1.0
N5 A:25S1485 4.8 50.6 1.0
SD A:MET106 4.8 43.1 1.0

Fluorine binding site 2 out of 3 in 4uqh

Go back to Fluorine Binding Sites List in 4uqh
Fluorine binding site 2 out of 3 in the Crystal Structure of Trypanosoma Cruzi CYP51 Bound to the Inhibitor (R)-N-(3-(1H-Indol-3-Yl)-1-Oxo-1-(Pyridin-4- Ylamino)Propan-2-Yl)-4-(4-(3,4-Difluorophenyl)Piperazin-1- Yl)-2-Fluorobenzamide.


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 Trypanosoma Cruzi CYP51 Bound to the Inhibitor (R)-N-(3-(1H-Indol-3-Yl)-1-Oxo-1-(Pyridin-4- Ylamino)Propan-2-Yl)-4-(4-(3,4-Difluorophenyl)Piperazin-1- Yl)-2-Fluorobenzamide. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F1485

b:74.7
occ:1.00
 F1 A:25S1485 0.0 74.7 1.0
C17 A:25S1485 1.3 62.0 1.0
C18 A:25S1485 2.3 61.1 1.0
C16 A:25S1485 2.5 62.8 1.0
F A:25S1485 2.8 71.2 1.0
C19 A:25S1485 3.5 58.8 1.0
CE A:MET358 3.6 66.7 1.0
C15 A:25S1485 3.7 55.2 1.0
CG1 A:VAL77 3.9 36.6 1.0
C14 A:25S1485 4.1 55.5 1.0
CD1 A:ILE70 4.1 51.5 1.0
CD1 A:ILE79 4.3 43.1 1.0
CZ A:PHE214 4.5 34.0 1.0
CD1 A:ILE72 4.5 33.6 1.0
CE1 A:PHE48 4.8 58.7 1.0
CG1 A:ILE79 4.8 43.3 1.0
CB A:VAL77 4.8 34.8 1.0
SD A:MET358 4.8 70.9 1.0
CG A:MET358 4.9 57.4 1.0
CD1 A:PHE48 5.0 57.2 1.0

Fluorine binding site 3 out of 3 in 4uqh

Go back to Fluorine Binding Sites List in 4uqh
Fluorine binding site 3 out of 3 in the Crystal Structure of Trypanosoma Cruzi CYP51 Bound to the Inhibitor (R)-N-(3-(1H-Indol-3-Yl)-1-Oxo-1-(Pyridin-4- Ylamino)Propan-2-Yl)-4-(4-(3,4-Difluorophenyl)Piperazin-1- Yl)-2-Fluorobenzamide.


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 Trypanosoma Cruzi CYP51 Bound to the Inhibitor (R)-N-(3-(1H-Indol-3-Yl)-1-Oxo-1-(Pyridin-4- Ylamino)Propan-2-Yl)-4-(4-(3,4-Difluorophenyl)Piperazin-1- Yl)-2-Fluorobenzamide. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F1485

b:71.2
occ:1.00
 F A:25S1485 0.0 71.2 1.0
C16 A:25S1485 1.4 62.8 1.0
C15 A:25S1485 2.4 55.2 1.0
C17 A:25S1485 2.4 62.0 1.0
F1 A:25S1485 2.8 74.7 1.0
CG A:PHE48 3.3 59.2 1.0
CD1 A:PHE48 3.4 57.2 1.0
CB A:PHE48 3.6 63.9 1.0
C14 A:25S1485 3.7 55.5 1.0
C18 A:25S1485 3.7 61.1 1.0
CD2 A:PHE48 3.9 58.4 1.0
CD1 A:ILE72 3.9 33.6 1.0
CE1 A:PHE48 4.0 58.7 1.0
C19 A:25S1485 4.2 58.8 1.0
CE2 A:PHE48 4.4 53.1 1.0
CZ A:PHE48 4.4 55.7 1.0
O A:HIS44 4.7 37.9 1.0
CZ A:PHE214 4.8 34.0 1.0
CD1 A:ILE70 4.8 51.5 1.0
CE2 A:PHE214 4.9 35.8 1.0
N4 A:25S1485 4.9 48.4 1.0
CA A:ILE45 5.0 41.1 1.0
CE A:MET358 5.0 66.7 1.0

Reference:

C.M.Calvet, D.F.Vieira, J.Y.Choi, D.Kellar, M.D.Cameron, J.L.Siqueira-Neto, J.Gut, J.B.Johnston, L.Lin, S.Khan, J.H.Mckerrow, W.R.Roush, L.M.Podust. 4-Aminopyridyl-Based CYP51 Inhibitors As Anti-Trypanosoma Cruzi Drug Leads with Improved Pharmacokinetic Profile and in Vivo Potency. J.Med.Chem. V. 57 6989 2014.
ISSN: ISSN 0022-2623
PubMed: 25101801
DOI: 10.1021/JM500448U
Page generated: Sun Dec 13 12:13:31 2020

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