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Iron in PDB 4bmm: 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)- 2',3,5'-Trifluoro-(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)- 2',3,5'-Trifluoro-(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)- 2',3,5'-Trifluoro-(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)- 2',3,5'-Trifluoro-(1,1'-Biphenyl)-4-Carboxamide, PDB code: 4bmm was solved by J.Y.Choi, C.M.Calvet, S.S.Gunatilleke, W.R.Roush, J.H.Mckerrow, L.M.Podust, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 114.63 / 2.84
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 272.469, 66.452, 122.219, 90.00, 110.65, 90.00
R / Rfree (%) 18.908 / 29.005

Other elements in 4bmm:

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)- 2',3,5'-Trifluoro-(1,1'-Biphenyl)-4-Carboxamide also contains other interesting chemical elements:

Fluorine (F) 12 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)- 2',3,5'-Trifluoro-(1,1'-Biphenyl)-4-Carboxamide (pdb code 4bmm). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 4 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)- 2',3,5'-Trifluoro-(1,1'-Biphenyl)-4-Carboxamide, PDB code: 4bmm:
Jump to Iron binding site number: 1; 2; 3; 4;

Iron binding site 1 out of 4 in 4bmm

Go back to Iron Binding Sites List in 4bmm
Iron binding site 1 out of 4 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)- 2',3,5'-Trifluoro-(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)- 2',3,5'-Trifluoro-(1,1'-Biphenyl)-4-Carboxamide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe1450

b:52.3
occ:1.00
 FE A:HEM1450 0.0 52.3 1.0
ND A:HEM1450 1.9 53.6 1.0
NA A:HEM1450 2.0 51.0 1.0
SG A:CYS422 2.0 53.7 1.0
NB A:HEM1450 2.1 49.2 1.0
NC A:HEM1450 2.1 51.4 1.0
N1 A:TU11460 2.1 51.7 1.0
C3 A:TU11460 2.9 52.5 1.0
C1D A:HEM1450 2.9 52.5 1.0
C4D A:HEM1450 2.9 53.6 1.0
C1A A:HEM1450 3.0 52.2 1.0
C4B A:HEM1450 3.0 50.1 1.0
C4A A:HEM1450 3.0 49.8 1.0
C1B A:HEM1450 3.0 48.1 1.0
C1C A:HEM1450 3.1 50.9 1.0
C4C A:HEM1450 3.1 51.9 1.0
C2 A:TU11460 3.2 51.9 1.0
CHA A:HEM1450 3.3 52.8 1.0
CHC A:HEM1450 3.4 50.5 1.0
CB A:CYS422 3.4 53.1 1.0
CHD A:HEM1450 3.4 51.4 1.0
CHB A:HEM1450 3.4 48.5 1.0
C2A A:HEM1450 4.2 51.8 1.0
C3A A:HEM1450 4.2 50.7 1.0
C2D A:HEM1450 4.2 54.0 1.0
C4 A:TU11460 4.2 53.5 1.0
C3D A:HEM1450 4.2 53.7 1.0
C3B A:HEM1450 4.2 49.7 1.0
C2B A:HEM1450 4.3 48.2 1.0
C2C A:HEM1450 4.3 51.0 1.0
C3C A:HEM1450 4.3 51.4 1.0
CA A:CYS422 4.3 53.0 1.0
C1 A:TU11460 4.5 52.0 1.0
C5 A:TU11460 4.9 52.8 1.0
C A:CYS422 5.0 52.0 1.0

Iron binding site 2 out of 4 in 4bmm

Go back to Iron Binding Sites List in 4bmm
Iron binding site 2 out of 4 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)- 2',3,5'-Trifluoro-(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)- 2',3,5'-Trifluoro-(1,1'-Biphenyl)-4-Carboxamide within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe1450

b:58.0
occ:1.00
 FE B:HEM1450 0.0 58.0 1.0
ND B:HEM1450 1.9 59.5 1.0
NA B:HEM1450 2.0 57.3 1.0
NC B:HEM1450 2.1 59.1 1.0
NB B:HEM1450 2.1 57.3 1.0
N1 B:TU11460 2.2 60.6 1.0
SG B:CYS422 2.2 60.7 1.0
C4D B:HEM1450 2.9 60.1 1.0
C1D B:HEM1450 2.9 59.8 1.0
C1A B:HEM1450 2.9 58.1 1.0
C2 B:TU11460 3.0 60.4 1.0
C4B B:HEM1450 3.0 58.3 1.0
C4A B:HEM1450 3.0 56.5 1.0
C1C B:HEM1450 3.1 59.7 1.0
C1B B:HEM1450 3.1 57.0 1.0
C4C B:HEM1450 3.1 60.0 1.0
C3 B:TU11460 3.2 61.4 1.0
CHA B:HEM1450 3.3 58.5 1.0
CHC B:HEM1450 3.4 58.4 1.0
CHD B:HEM1450 3.4 59.0 1.0
CHB B:HEM1450 3.5 56.3 1.0
CB B:CYS422 3.6 61.3 1.0
C3D B:HEM1450 4.2 60.5 1.0
C2D B:HEM1450 4.2 59.6 1.0
C2A B:HEM1450 4.2 58.1 1.0
C3A B:HEM1450 4.2 57.6 1.0
CA B:CYS422 4.3 61.1 1.0
C3B B:HEM1450 4.3 58.0 1.0
C2C B:HEM1450 4.3 59.5 1.0
C3C B:HEM1450 4.3 59.1 1.0
C2B B:HEM1450 4.3 57.9 1.0
C1 B:TU11460 4.3 61.6 1.0
C4 B:TU11460 4.4 63.2 1.0
CB B:ALA291 4.8 59.9 1.0
N B:ILE423 4.9 63.3 1.0
N B:GLY424 4.9 59.1 1.0
C5 B:TU11460 4.9 61.9 1.0

Iron binding site 3 out of 4 in 4bmm

Go back to Iron Binding Sites List in 4bmm
Iron binding site 3 out of 4 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)- 2',3,5'-Trifluoro-(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 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)- 2',3,5'-Trifluoro-(1,1'-Biphenyl)-4-Carboxamide within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Fe1450

b:60.9
occ:1.00
 FE C:HEM1450 0.0 60.9 1.0
ND C:HEM1450 1.9 61.1 1.0
NA C:HEM1450 2.0 60.6 1.0
SG C:CYS422 2.1 61.4 1.0
NC C:HEM1450 2.1 63.8 1.0
NB C:HEM1450 2.1 61.3 1.0
N1 C:TU11460 2.1 61.4 1.0
C1D C:HEM1450 2.9 62.6 1.0
C4D C:HEM1450 2.9 61.4 1.0
C2 C:TU11460 3.0 62.7 1.0
C4A C:HEM1450 3.0 61.4 1.0
C1A C:HEM1450 3.0 61.1 1.0
C1B C:HEM1450 3.0 61.9 1.0
C4C C:HEM1450 3.0 64.4 1.0
C4B C:HEM1450 3.1 61.4 1.0
C3 C:TU11460 3.1 64.0 1.0
C1C C:HEM1450 3.1 65.4 1.0
CHD C:HEM1450 3.4 63.7 1.0
CHB C:HEM1450 3.4 63.0 1.0
CHA C:HEM1450 3.4 62.0 1.0
CB C:CYS422 3.4 63.6 1.0
CHC C:HEM1450 3.5 62.6 1.0
C2D C:HEM1450 4.2 65.3 1.0
C2A C:HEM1450 4.2 61.6 1.0
C3A C:HEM1450 4.2 62.2 1.0
C3D C:HEM1450 4.2 64.6 1.0
CA C:CYS422 4.3 64.1 1.0
C3C C:HEM1450 4.3 66.5 1.0
C2B C:HEM1450 4.3 62.4 1.0
C2C C:HEM1450 4.3 68.3 1.0
C1 C:TU11460 4.3 64.6 1.0
C3B C:HEM1450 4.3 61.5 1.0
C4 C:TU11460 4.4 64.1 1.0
N C:GLY424 4.8 67.2 1.0
C5 C:TU11460 4.9 61.9 1.0
C C:CYS422 4.9 64.8 1.0

Iron binding site 4 out of 4 in 4bmm

Go back to Iron Binding Sites List in 4bmm
Iron binding site 4 out of 4 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)- 2',3,5'-Trifluoro-(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 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)- 2',3,5'-Trifluoro-(1,1'-Biphenyl)-4-Carboxamide within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Fe1450

b:53.2
occ:1.00
 FE D:HEM1450 0.0 53.2 1.0
ND D:HEM1450 1.9 52.0 1.0
NA D:HEM1450 2.0 51.8 1.0
NB D:HEM1450 2.1 52.7 1.0
NC D:HEM1450 2.1 53.0 1.0
N1 D:TU11460 2.1 52.7 1.0
SG D:CYS422 2.3 51.5 1.0
C1D D:HEM1450 2.9 52.0 1.0
C4D D:HEM1450 2.9 51.9 1.0
C1A D:HEM1450 3.0 52.8 1.0
C4A D:HEM1450 3.0 50.9 1.0
C3 D:TU11460 3.0 52.6 1.0
C2 D:TU11460 3.0 52.8 1.0
C4B D:HEM1450 3.0 52.3 1.0
C1B D:HEM1450 3.0 52.3 1.0
C4C D:HEM1450 3.1 53.6 1.0
C1C D:HEM1450 3.1 54.0 1.0
CB D:CYS422 3.2 51.3 1.0
CHA D:HEM1450 3.4 53.4 1.0
CHD D:HEM1450 3.4 53.0 1.0
CHB D:HEM1450 3.4 51.0 1.0
CHC D:HEM1450 3.4 52.3 1.0
CA D:CYS422 4.0 51.6 1.0
C2D D:HEM1450 4.2 52.3 1.0
C3D D:HEM1450 4.2 52.1 1.0
C3A D:HEM1450 4.2 51.1 1.0
C2A D:HEM1450 4.2 51.9 1.0
C2B D:HEM1450 4.3 53.2 1.0
C2C D:HEM1450 4.3 55.2 1.0
C3B D:HEM1450 4.3 52.1 1.0
C3C D:HEM1450 4.3 55.9 1.0
C4 D:TU11460 4.3 53.1 1.0
C1 D:TU11460 4.3 54.0 1.0
C D:CYS422 4.8 51.7 1.0
C5 D:TU11460 4.9 53.7 1.0
N D:ILE423 4.9 50.8 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: Mon Aug 5 00:07:44 2024

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