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Iron in PDB 4by0: 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)-3,3'-Difluoro-(1,1'-Biphenyl)-4- Carboxamide

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)-3,3'-Difluoro-(1,1'-Biphenyl)-4- Carboxamide

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)-3,3'-Difluoro-(1,1'-Biphenyl)-4- Carboxamide:
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)-3,3'-Difluoro-(1,1'-Biphenyl)-4- Carboxamide, PDB code: 4by0 was solved by J.Y.Choi, C.M.Calvet, D.F.Vieira, S.S.Gunatilleke, M.D.Cameron, J.H.Mckerrow, L.M.Podust, W.R.Roush, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 80.16 / 3.10
Space group P 32 2 1
Cell size a, b, c (Å), α, β, γ (°) 124.167, 124.167, 119.839, 90.00, 90.00, 120.00
R / Rfree (%) 23.195 / 29.748

Other elements in 4by0:

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)-3,3'-Difluoro-(1,1'-Biphenyl)-4- Carboxamide also contains other interesting chemical elements:

Fluorine (F) 4 atoms

Iron Binding Sites:

The binding sites of Iron 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)-3,3'-Difluoro-(1,1'-Biphenyl)-4- Carboxamide (pdb code 4by0). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 2 binding sites of Iron 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)-3,3'-Difluoro-(1,1'-Biphenyl)-4- Carboxamide, PDB code: 4by0:
Jump to Iron binding site number: 1; 2;

Iron binding site 1 out of 2 in 4by0

Go back to Iron Binding Sites List in 4by0
Iron binding site 1 out of 2 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)-3,3'-Difluoro-(1,1'-Biphenyl)-4- Carboxamide


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe 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)-3,3'-Difluoro-(1,1'-Biphenyl)-4- Carboxamide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe1450

b:43.2
occ:1.00
 FE A:HEM1450 0.0 43.2 1.0
ND A:HEM1450 1.9 45.2 1.0
NA A:HEM1450 2.0 45.0 1.0
N1 A:5PS1460 2.0 62.4 1.0
SG A:CYS422 2.0 45.7 1.0
NC A:HEM1450 2.1 42.0 1.0
NB A:HEM1450 2.1 45.0 1.0
C1D A:HEM1450 2.8 44.0 1.0
C4D A:HEM1450 2.9 50.1 1.0
C3 A:5PS1460 2.9 63.4 1.0
C2 A:5PS1460 2.9 65.7 1.0
C1A A:HEM1450 3.0 49.3 1.0
C4B A:HEM1450 3.0 45.8 1.0
C4A A:HEM1450 3.0 45.4 1.0
C4C A:HEM1450 3.0 42.8 1.0
C1C A:HEM1450 3.0 42.5 1.0
C1B A:HEM1450 3.1 46.8 1.0
CB A:CYS422 3.3 48.2 1.0
CHD A:HEM1450 3.3 42.4 1.0
CHA A:HEM1450 3.4 49.4 1.0
CHC A:HEM1450 3.4 43.6 1.0
CHB A:HEM1450 3.5 45.0 1.0
CA A:CYS422 4.0 50.0 1.0
C2D A:HEM1450 4.1 48.8 1.0
C3D A:HEM1450 4.1 50.9 1.0
C2A A:HEM1450 4.2 51.0 1.0
C4 A:5PS1460 4.2 63.4 1.0
C3A A:HEM1450 4.2 46.8 1.0
C1 A:5PS1460 4.2 66.0 1.0
C3C A:HEM1450 4.3 44.6 1.0
C3B A:HEM1450 4.3 51.0 1.0
C2C A:HEM1450 4.3 42.9 1.0
C2B A:HEM1450 4.3 48.5 1.0
C5 A:5PS1460 4.8 62.6 1.0
CB A:ALA291 4.8 54.6 1.0
N A:ILE423 4.8 47.1 1.0
C A:CYS422 4.9 49.8 1.0
N A:GLY424 5.0 54.5 1.0

Iron binding site 2 out of 2 in 4by0

Go back to Iron Binding Sites List in 4by0
Iron binding site 2 out of 2 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)-3,3'-Difluoro-(1,1'-Biphenyl)-4- Carboxamide


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe 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)-3,3'-Difluoro-(1,1'-Biphenyl)-4- Carboxamide within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe1450

b:69.5
occ:1.00
 FE B:HEM1450 0.0 69.5 1.0
N1 B:5PS1460 1.9 69.7 1.0
ND B:HEM1450 1.9 75.2 1.0
NA B:HEM1450 2.0 67.1 1.0
NC B:HEM1450 2.1 61.5 1.0
NB B:HEM1450 2.1 72.5 1.0
SG B:CYS422 2.1 66.6 1.0
C3 B:5PS1460 2.7 74.5 1.0
C2 B:5PS1460 2.8 69.7 1.0
C1D B:HEM1450 2.9 73.4 1.0
C4D B:HEM1450 2.9 77.4 1.0
C1A B:HEM1450 2.9 70.6 1.0
C4A B:HEM1450 3.0 69.6 1.0
C4B B:HEM1450 3.0 71.6 1.0
C4C B:HEM1450 3.0 64.4 1.0
C1B B:HEM1450 3.0 72.5 1.0
C1C B:HEM1450 3.1 62.8 1.0
CB B:CYS422 3.3 76.4 1.0
CHA B:HEM1450 3.3 76.9 1.0
CHD B:HEM1450 3.4 68.1 1.0
CHB B:HEM1450 3.4 70.0 1.0
CHC B:HEM1450 3.4 67.9 1.0
C4 B:5PS1460 4.1 74.0 1.0
CA B:CYS422 4.1 76.2 1.0
C1 B:5PS1460 4.1 73.6 1.0
C2A B:HEM1450 4.1 70.7 1.0
C3A B:HEM1450 4.1 68.5 1.0
C2D B:HEM1450 4.1 76.8 1.0
C3D B:HEM1450 4.2 78.7 1.0
C3C B:HEM1450 4.2 65.2 1.0
C2C B:HEM1450 4.3 64.6 1.0
C2B B:HEM1450 4.3 73.1 1.0
C3B B:HEM1450 4.3 71.0 1.0
N B:GLY424 4.5 76.4 1.0
C5 B:5PS1460 4.6 71.2 1.0
CA B:GLY424 4.6 76.6 1.0
C B:CYS422 4.9 71.9 1.0

Reference:

J.Y.Choi, C.M.Calvet, D.F.Vieira, S.S.Gunatilleke, M.D.Cameron, J.H.Mckerrow, L.M.Podust, W.R.Roush. R-Configuration of 4-Aminopyridyl-Based Inhibitors of CYP51 Confers Superior Efficacy Against Trypanosoma Cruzi Acs Med.Chem.Lett. V. 5 434 2014.
ISSN: ISSN 1948-5875
PubMed: 24900854
DOI: 10.1021/ML500010M
Page generated: Mon Aug 5 00:13:13 2024

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