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Iron in PDB 4bjk: CYP51 of Trypanosoma Brucei Bound to (S)-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 CYP51 of Trypanosoma Brucei Bound to (S)-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 CYP51 of Trypanosoma Brucei Bound to (S)-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 CYP51 of Trypanosoma Brucei Bound to (S)-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: 4bjk was solved by L.M.Podust, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 87.88 / 2.67
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 199.291, 114.671, 136.221, 90.00, 132.47, 90.00
R / Rfree (%) 19.442 / 27.352

Other elements in 4bjk:

The structure of CYP51 of Trypanosoma Brucei Bound to (S)-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) 2 atoms

Iron Binding Sites:

The binding sites of Iron atom in the CYP51 of Trypanosoma Brucei Bound to (S)-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 4bjk). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 4 binding sites of Iron where determined in the CYP51 of Trypanosoma Brucei Bound to (S)-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: 4bjk:
Jump to Iron binding site number: 1; 2; 3; 4;

Iron binding site 1 out of 4 in 4bjk

Go back to Iron Binding Sites List in 4bjk
Iron binding site 1 out of 4 in the CYP51 of Trypanosoma Brucei Bound to (S)-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 CYP51 of Trypanosoma Brucei Bound to (S)-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:45.6
occ:1.00
 FE A:HEM1450 0.0 45.6 1.0
N1 A:18I1460 1.9 57.4 1.0
ND A:HEM1450 1.9 50.6 1.0
NA A:HEM1450 2.0 45.2 1.0
NB A:HEM1450 2.1 44.4 1.0
NC A:HEM1450 2.1 48.1 1.0
SG A:CYS422 2.3 47.8 1.0
C2 A:18I1460 2.7 61.2 1.0
C1D A:HEM1450 2.9 49.3 1.0
C3 A:18I1460 2.9 59.0 1.0
C4D A:HEM1450 2.9 48.5 1.0
C1A A:HEM1450 3.0 46.6 1.0
C4B A:HEM1450 3.0 51.6 1.0
C4A A:HEM1450 3.0 48.4 1.0
C4C A:HEM1450 3.0 51.6 1.0
C1B A:HEM1450 3.0 46.3 1.0
C1C A:HEM1450 3.1 47.3 1.0
CB A:CYS422 3.3 51.3 1.0
CHA A:HEM1450 3.3 52.4 1.0
CHD A:HEM1450 3.4 48.5 1.0
CHB A:HEM1450 3.4 52.8 1.0
CHC A:HEM1450 3.4 48.7 1.0
C1 A:18I1460 4.0 59.0 1.0
CA A:CYS422 4.1 52.1 1.0
C2A A:HEM1450 4.2 44.5 1.0
C2D A:HEM1450 4.2 50.5 1.0
C3D A:HEM1450 4.2 50.4 1.0
C3A A:HEM1450 4.2 45.0 1.0
C4 A:18I1460 4.2 55.0 1.0
C3C A:HEM1450 4.2 50.2 1.0
C3B A:HEM1450 4.2 45.1 1.0
C2B A:HEM1450 4.3 44.1 1.0
C2C A:HEM1450 4.3 46.3 1.0
C5 A:18I1460 4.7 61.7 1.0
N A:GLY424 4.9 45.1 1.0
N A:ILE423 4.9 50.9 1.0
C A:CYS422 4.9 48.5 1.0

Iron binding site 2 out of 4 in 4bjk

Go back to Iron Binding Sites List in 4bjk
Iron binding site 2 out of 4 in the CYP51 of Trypanosoma Brucei Bound to (S)-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 CYP51 of Trypanosoma Brucei Bound to (S)-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:47.7
occ:1.00
 FE B:HEM1450 0.0 47.7 1.0
ND B:HEM1450 1.9 48.0 1.0
NA B:HEM1450 2.0 41.0 1.0
NC B:HEM1450 2.1 44.3 1.0
NB B:HEM1450 2.1 42.7 1.0
N1 B:18I1460 2.2 76.1 1.0
SG B:CYS422 2.3 51.7 1.0
C1D B:HEM1450 2.9 45.6 1.0
C4D B:HEM1450 2.9 49.7 1.0
C4A B:HEM1450 3.0 40.0 1.0
C1B B:HEM1450 3.0 45.2 1.0
C4B B:HEM1450 3.0 48.6 1.0
C4C B:HEM1450 3.0 43.8 1.0
C1A B:HEM1450 3.0 46.6 1.0
C2 B:18I1460 3.0 75.8 1.0
C3 B:18I1460 3.1 71.6 1.0
C1C B:HEM1450 3.1 46.3 1.0
CHB B:HEM1450 3.3 46.2 1.0
CHD B:HEM1450 3.3 44.9 1.0
CB B:CYS422 3.4 54.3 1.0
CHA B:HEM1450 3.4 48.6 1.0
CHC B:HEM1450 3.5 46.6 1.0
CA B:CYS422 4.1 52.6 1.0
C2D B:HEM1450 4.1 46.2 1.0
C3D B:HEM1450 4.1 50.4 1.0
C3A B:HEM1450 4.2 41.4 1.0
C2A B:HEM1450 4.2 44.7 1.0
C3C B:HEM1450 4.2 44.6 1.0
C2B B:HEM1450 4.2 45.7 1.0
C3B B:HEM1450 4.3 48.1 1.0
C2C B:HEM1450 4.3 45.8 1.0
C1 B:18I1460 4.3 70.9 1.0
C4 B:18I1460 4.4 71.7 1.0
N B:GLY424 4.8 43.1 1.0
C5 B:18I1460 4.9 75.1 1.0
C B:CYS422 5.0 50.2 1.0
N B:ILE423 5.0 44.3 1.0

Iron binding site 3 out of 4 in 4bjk

Go back to Iron Binding Sites List in 4bjk
Iron binding site 3 out of 4 in the CYP51 of Trypanosoma Brucei Bound to (S)-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 3 of CYP51 of Trypanosoma Brucei Bound to (S)-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
C:Fe1450

b:50.9
occ:1.00
 FE C:HEM1450 0.0 50.9 1.0
N1 C:18I1460 1.6 73.5 1.0
ND C:HEM1450 1.9 53.6 1.0
NA C:HEM1450 2.0 47.5 1.0
NB C:HEM1450 2.1 48.3 1.0
NC C:HEM1450 2.1 52.2 1.0
SG C:CYS422 2.3 47.4 1.0
C3 C:18I1460 2.4 79.5 1.0
C2 C:18I1460 2.7 72.3 1.0
C4D C:HEM1450 2.9 51.5 1.0
C1D C:HEM1450 2.9 51.2 1.0
C1A C:HEM1450 3.0 48.3 1.0
C4B C:HEM1450 3.0 48.9 1.0
C1B C:HEM1450 3.0 49.4 1.0
C4A C:HEM1450 3.0 46.0 1.0
C4C C:HEM1450 3.0 54.6 1.0
C1C C:HEM1450 3.1 51.9 1.0
CB C:CYS422 3.3 52.4 1.0
CHA C:HEM1450 3.4 48.4 1.0
CHD C:HEM1450 3.4 53.8 1.0
CHB C:HEM1450 3.4 46.3 1.0
CHC C:HEM1450 3.4 47.6 1.0
C4 C:18I1460 3.7 75.9 1.0
C1 C:18I1460 4.0 67.3 1.0
CA C:CYS422 4.1 53.2 1.0
C2D C:HEM1450 4.1 51.5 1.0
C3D C:HEM1450 4.2 55.5 1.0
C3A C:HEM1450 4.2 45.5 1.0
C2A C:HEM1450 4.2 49.3 1.0
C2B C:HEM1450 4.2 53.9 1.0
C3B C:HEM1450 4.2 52.6 1.0
C3C C:HEM1450 4.2 57.5 1.0
C2C C:HEM1450 4.3 55.7 1.0
C5 C:18I1460 4.4 71.3 1.0
N C:ILE423 4.8 58.1 1.0
C C:CYS422 4.8 56.5 1.0
N C:GLY424 4.9 56.8 1.0

Iron binding site 4 out of 4 in 4bjk

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Iron binding site 4 out of 4 in the CYP51 of Trypanosoma Brucei Bound to (S)-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 4 of CYP51 of Trypanosoma Brucei Bound to (S)-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
D:Fe1450

b:56.9
occ:1.00
 FE D:HEM1450 0.0 56.9 1.0
ND D:HEM1450 1.9 64.1 1.0
NA D:HEM1450 2.0 59.1 1.0
NC D:HEM1450 2.1 53.8 1.0
NB D:HEM1450 2.1 54.6 1.0
SG D:CYS422 2.4 53.8 1.0
N1 D:18I1460 2.6 74.4 1.0
C4D D:HEM1450 2.9 66.0 1.0
C1D D:HEM1450 2.9 65.8 1.0
C1A D:HEM1450 3.0 63.9 1.0
C4A D:HEM1450 3.0 61.9 1.0
C4B D:HEM1450 3.0 54.2 1.0
C4C D:HEM1450 3.0 58.9 1.0
C1C D:HEM1450 3.0 53.3 1.0
C1B D:HEM1450 3.0 54.6 1.0
CHA D:HEM1450 3.3 68.6 1.0
CHC D:HEM1450 3.4 55.2 1.0
CHD D:HEM1450 3.4 60.5 1.0
CHB D:HEM1450 3.4 56.4 1.0
CB D:CYS422 3.4 53.8 1.0
C2 D:18I1460 3.4 77.8 1.0
C3 D:18I1460 3.5 80.6 1.0
C3D D:HEM1450 4.1 65.9 1.0
C2D D:HEM1450 4.1 68.5 1.0
C2A D:HEM1450 4.2 67.4 1.0
C3A D:HEM1450 4.2 64.7 1.0
CA D:CYS422 4.2 55.0 1.0
C3C D:HEM1450 4.2 58.9 1.0
C2C D:HEM1450 4.2 55.6 1.0
C3B D:HEM1450 4.3 54.3 1.0
C2B D:HEM1450 4.3 56.5 1.0
C1 D:18I1460 4.8 78.0 1.0
CB D:ALA291 4.8 65.3 1.0
C4 D:18I1460 4.8 73.6 1.0
C D:CYS422 4.9 55.5 1.0
N D:ILE423 4.9 55.0 1.0
N D:GLY424 5.0 48.3 1.0

Reference:

J.Y.Choi, C.M.Calvet, S.S.Gunatilleke, C.Ruiz, M.D.Cameron, J.H.Mckerrow, L.M.Podust, W.R.Roush. Rational Development of 4-Aminopyridyl-Based Inhibitors Targeting Trypanosoma Cruzi CYP51 As Anti-Chagas Agents. J.Med.Chem. V. 56 7651 2013.
ISSN: ISSN 0022-2623
PubMed: 24079662
DOI: 10.1021/JM401067S
Page generated: Mon Aug 5 00:03:28 2024

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