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Fluorine in PDB 4ytn: Crystal Structure of Mitochondrial Rhodoquinol-Fumarate Reductase From Ascaris Suum with N-[3-(Pentafluorophenoxy)Phenyl]-2- (Trifluoromethyl)Benzamide

Enzymatic activity of Crystal Structure of Mitochondrial Rhodoquinol-Fumarate Reductase From Ascaris Suum with N-[3-(Pentafluorophenoxy)Phenyl]-2- (Trifluoromethyl)Benzamide

All present enzymatic activity of Crystal Structure of Mitochondrial Rhodoquinol-Fumarate Reductase From Ascaris Suum with N-[3-(Pentafluorophenoxy)Phenyl]-2- (Trifluoromethyl)Benzamide:
1.3.5.1;

Protein crystallography data

The structure of Crystal Structure of Mitochondrial Rhodoquinol-Fumarate Reductase From Ascaris Suum with N-[3-(Pentafluorophenoxy)Phenyl]-2- (Trifluoromethyl)Benzamide, PDB code: 4ytn was solved by S.Harada, T.Shiba, D.Sato, A.Yamamoto, M.Nagahama, A.Yone, D.K.Inaoka, K.Sakamoto, M.Inoue, T.Honma, K.Kita, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 20.00 / 3.00
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 123.614, 125.483, 219.670, 90.00, 90.00, 90.00
R / Rfree (%) 19 / 23.6

Other elements in 4ytn:

The structure of Crystal Structure of Mitochondrial Rhodoquinol-Fumarate Reductase From Ascaris Suum with N-[3-(Pentafluorophenoxy)Phenyl]-2- (Trifluoromethyl)Benzamide also contains other interesting chemical elements:

Iron (Fe) 20 atoms

Fluorine Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 16;

Binding sites:

The binding sites of Fluorine atom in the Crystal Structure of Mitochondrial Rhodoquinol-Fumarate Reductase From Ascaris Suum with N-[3-(Pentafluorophenoxy)Phenyl]-2- (Trifluoromethyl)Benzamide (pdb code 4ytn). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 16 binding sites of Fluorine where determined in the Crystal Structure of Mitochondrial Rhodoquinol-Fumarate Reductase From Ascaris Suum with N-[3-(Pentafluorophenoxy)Phenyl]-2- (Trifluoromethyl)Benzamide, PDB code: 4ytn:
Jump to Fluorine binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Fluorine binding site 1 out of 16 in 4ytn

Go back to Fluorine Binding Sites List in 4ytn
Fluorine binding site 1 out of 16 in the Crystal Structure of Mitochondrial Rhodoquinol-Fumarate Reductase From Ascaris Suum with N-[3-(Pentafluorophenoxy)Phenyl]-2- (Trifluoromethyl)Benzamide


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 Mitochondrial Rhodoquinol-Fumarate Reductase From Ascaris Suum with N-[3-(Pentafluorophenoxy)Phenyl]-2- (Trifluoromethyl)Benzamide within 5.0Å range:
probe atom residue distance (Å) B Occ
C:F202

b:0.4
occ:1.00
 F1 C:FD8202 0.0 0.4 1.0
C1 C:FD8202 1.3 0.1 1.0
F2 C:FD8202 2.1 0.4 1.0
F3 C:FD8202 2.2 0.7 1.0
C2 C:FD8202 2.3 0.7 1.0
NE1 B:TRP197 2.5 49.1 1.0
C3 C:FD8202 2.8 0.9 1.0
C8 C:FD8202 2.8 0.8 1.0
OH D:TYR107 2.8 69.6 1.0
CD1 B:TRP197 3.0 49.0 1.0
O1 C:FD8202 3.1 0.1 1.0
CE2 D:TYR107 3.3 68.7 1.0
N C:FD8202 3.4 0.0 1.0
CZ D:TYR107 3.4 68.4 1.0
C7 C:FD8202 3.5 0.2 1.0
CE2 B:TRP197 3.7 50.6 1.0
NH1 C:ARG76 3.8 65.2 1.0
C4 C:FD8202 4.2 0.4 1.0
C9 C:FD8202 4.3 0.9 1.0
CG B:TRP197 4.3 49.9 1.0
CZ2 B:TRP197 4.4 52.5 1.0
CB D:ASP106 4.5 58.6 1.0
CZ C:ARG76 4.5 63.2 1.0
C14 C:FD8202 4.5 0.9 1.0
CD2 D:TYR107 4.6 68.1 1.0
CB B:PRO193 4.6 46.5 1.0
CD2 B:TRP197 4.7 51.3 1.0
C6 C:FD8202 4.7 0.8 1.0
CE1 D:TYR107 4.7 67.4 1.0
CG D:ASP106 4.8 60.3 1.0
OD2 D:ASP106 4.8 59.2 1.0
C5 C:FD8202 4.9 0.7 1.0
CD C:ARG76 4.9 58.5 1.0
O B:PRO193 5.0 43.2 1.0

Fluorine binding site 2 out of 16 in 4ytn

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Fluorine binding site 2 out of 16 in the Crystal Structure of Mitochondrial Rhodoquinol-Fumarate Reductase From Ascaris Suum with N-[3-(Pentafluorophenoxy)Phenyl]-2- (Trifluoromethyl)Benzamide


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 Mitochondrial Rhodoquinol-Fumarate Reductase From Ascaris Suum with N-[3-(Pentafluorophenoxy)Phenyl]-2- (Trifluoromethyl)Benzamide within 5.0Å range:
probe atom residue distance (Å) B Occ
C:F202

b:0.4
occ:1.00
 F2 C:FD8202 0.0 0.4 1.0
C1 C:FD8202 1.3 0.1 1.0
F3 C:FD8202 2.1 0.7 1.0
F1 C:FD8202 2.1 0.4 1.0
C2 C:FD8202 2.2 0.7 1.0
NH1 C:ARG76 2.3 65.2 1.0
C7 C:FD8202 2.6 0.2 1.0
CZ C:ARG76 2.7 63.2 1.0
NH2 C:ARG76 3.2 63.1 1.0
OH D:TYR107 3.4 69.6 1.0
OD2 D:ASP106 3.4 59.2 1.0
C3 C:FD8202 3.5 0.9 1.0
NE C:ARG76 3.5 60.6 1.0
CG D:ASP106 3.9 60.3 1.0
C6 C:FD8202 3.9 0.8 1.0
CD C:ARG76 4.0 58.5 1.0
CZ D:TYR107 4.1 68.4 1.0
CB D:ASP106 4.1 58.6 1.0
C8 C:FD8202 4.2 0.8 1.0
NE1 B:TRP197 4.3 49.1 1.0
CD1 B:TRP197 4.3 49.0 1.0
CE2 D:TYR107 4.4 68.7 1.0
C4 C:FD8202 4.5 0.4 1.0
OD1 D:ASP106 4.7 63.3 1.0
C5 C:FD8202 4.7 0.7 1.0
N C:FD8202 4.7 0.0 1.0
CD2 B:HIS240 4.8 59.0 1.0
O1 C:FD8202 4.8 0.1 1.0
CE1 D:TYR107 5.0 67.4 1.0

Fluorine binding site 3 out of 16 in 4ytn

Go back to Fluorine Binding Sites List in 4ytn
Fluorine binding site 3 out of 16 in the Crystal Structure of Mitochondrial Rhodoquinol-Fumarate Reductase From Ascaris Suum with N-[3-(Pentafluorophenoxy)Phenyl]-2- (Trifluoromethyl)Benzamide


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 Mitochondrial Rhodoquinol-Fumarate Reductase From Ascaris Suum with N-[3-(Pentafluorophenoxy)Phenyl]-2- (Trifluoromethyl)Benzamide within 5.0Å range:
probe atom residue distance (Å) B Occ
C:F202

b:0.7
occ:1.00
 F3 C:FD8202 0.0 0.7 1.0
C1 C:FD8202 1.4 0.1 1.0
F2 C:FD8202 2.1 0.4 1.0
F1 C:FD8202 2.2 0.4 1.0
C2 C:FD8202 2.3 0.7 1.0
C7 C:FD8202 2.9 0.2 1.0
NE1 B:TRP197 3.4 49.1 1.0
C3 C:FD8202 3.4 0.9 1.0
CD1 B:TRP197 3.4 49.0 1.0
N B:SER194 3.6 45.8 1.0
CA B:SER194 3.8 48.7 1.0
C B:PRO193 3.8 45.8 1.0
CB B:PRO193 3.9 46.5 1.0
CD1 B:ILE242 4.0 47.9 1.0
C8 C:FD8202 4.0 0.8 1.0
O B:PRO193 4.1 43.2 1.0
C6 C:FD8202 4.1 0.8 1.0
O1 C:FD8202 4.2 0.1 1.0
NH1 C:ARG76 4.4 65.2 1.0
OD2 D:ASP106 4.4 59.2 1.0
CG D:ASP106 4.4 60.3 1.0
CB B:SER194 4.4 50.4 1.0
CA B:PRO193 4.5 46.8 1.0
C4 C:FD8202 4.5 0.4 1.0
OD1 D:ASP106 4.7 63.3 1.0
CE2 B:TRP197 4.7 50.6 1.0
CG B:TRP197 4.7 49.9 1.0
CZ C:ARG76 4.8 63.2 1.0
OH D:TYR107 4.8 69.6 1.0
C5 C:FD8202 4.8 0.7 1.0
OG B:SER194 4.8 54.3 1.0
CB D:ASP106 4.9 58.6 1.0
NH2 C:ARG76 4.9 63.1 1.0
CG B:PRO193 5.0 47.6 1.0

Fluorine binding site 4 out of 16 in 4ytn

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Fluorine binding site 4 out of 16 in the Crystal Structure of Mitochondrial Rhodoquinol-Fumarate Reductase From Ascaris Suum with N-[3-(Pentafluorophenoxy)Phenyl]-2- (Trifluoromethyl)Benzamide


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 Mitochondrial Rhodoquinol-Fumarate Reductase From Ascaris Suum with N-[3-(Pentafluorophenoxy)Phenyl]-2- (Trifluoromethyl)Benzamide within 5.0Å range:
probe atom residue distance (Å) B Occ
C:F202

b:0.9
occ:1.00
 F4 C:FD8202 0.0 0.9 1.0
C16 C:FD8202 1.4 0.2 1.0
C17 C:FD8202 2.4 0.6 1.0
C15 C:FD8202 2.4 0.7 1.0
F5 C:FD8202 2.8 0.6 1.0
O2 C:FD8202 2.8 0.3 1.0
C12 C:FD8202 3.2 0.6 1.0
CD1 C:LEU60 3.3 67.3 1.0
C13 C:FD8202 3.4 0.9 1.0
C18 C:FD8202 3.7 1.0 1.0
C20 C:FD8202 3.7 0.6 1.0
C19 C:FD8202 4.2 0.4 1.0
C11 C:FD8202 4.4 0.8 1.0
C14 C:FD8202 4.7 0.9 1.0
F8 C:FD8202 4.8 0.8 1.0
F6 C:FD8202 4.8 0.6 1.0
CG C:LEU60 4.8 67.5 1.0

Fluorine binding site 5 out of 16 in 4ytn

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Fluorine binding site 5 out of 16 in the Crystal Structure of Mitochondrial Rhodoquinol-Fumarate Reductase From Ascaris Suum with N-[3-(Pentafluorophenoxy)Phenyl]-2- (Trifluoromethyl)Benzamide


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 Mitochondrial Rhodoquinol-Fumarate Reductase From Ascaris Suum with N-[3-(Pentafluorophenoxy)Phenyl]-2- (Trifluoromethyl)Benzamide within 5.0Å range:
probe atom residue distance (Å) B Occ
C:F202

b:0.6
occ:1.00
 F5 C:FD8202 0.0 0.6 1.0
C17 C:FD8202 1.4 0.6 1.0
C16 C:FD8202 2.4 0.2 1.0
C18 C:FD8202 2.4 1.0 1.0
F4 C:FD8202 2.8 0.9 1.0
F6 C:FD8202 2.8 0.6 1.0
C15 C:FD8202 3.7 0.7 1.0
C19 C:FD8202 3.7 0.4 1.0
C20 C:FD8202 4.2 0.6 1.0
CD1 C:LEU60 4.5 67.3 1.0
O2 C:FD8202 4.8 0.3 1.0
F7 C:FD8202 4.8 0.6 1.0

Fluorine binding site 6 out of 16 in 4ytn

Go back to Fluorine Binding Sites List in 4ytn
Fluorine binding site 6 out of 16 in the Crystal Structure of Mitochondrial Rhodoquinol-Fumarate Reductase From Ascaris Suum with N-[3-(Pentafluorophenoxy)Phenyl]-2- (Trifluoromethyl)Benzamide


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 Mitochondrial Rhodoquinol-Fumarate Reductase From Ascaris Suum with N-[3-(Pentafluorophenoxy)Phenyl]-2- (Trifluoromethyl)Benzamide within 5.0Å range:
probe atom residue distance (Å) B Occ
C:F202

b:0.6
occ:1.00
 F6 C:FD8202 0.0 0.6 1.0
C18 C:FD8202 1.4 1.0 1.0
C19 C:FD8202 2.4 0.4 1.0
C17 C:FD8202 2.4 0.6 1.0
F7 C:FD8202 2.8 0.6 1.0
F5 C:FD8202 2.8 0.6 1.0
NH1 D:ARG109 3.4 73.4 1.0
C20 C:FD8202 3.7 0.6 1.0
C16 C:FD8202 3.7 0.2 1.0
C15 C:FD8202 4.2 0.7 1.0
CZ D:ARG109 4.7 70.9 1.0
F8 C:FD8202 4.8 0.8 1.0
F4 C:FD8202 4.8 0.9 1.0

Fluorine binding site 7 out of 16 in 4ytn

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Fluorine binding site 7 out of 16 in the Crystal Structure of Mitochondrial Rhodoquinol-Fumarate Reductase From Ascaris Suum with N-[3-(Pentafluorophenoxy)Phenyl]-2- (Trifluoromethyl)Benzamide


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 7 of Crystal Structure of Mitochondrial Rhodoquinol-Fumarate Reductase From Ascaris Suum with N-[3-(Pentafluorophenoxy)Phenyl]-2- (Trifluoromethyl)Benzamide within 5.0Å range:
probe atom residue distance (Å) B Occ
C:F202

b:0.6
occ:1.00
 F7 C:FD8202 0.0 0.6 1.0
C19 C:FD8202 1.4 0.4 1.0
C18 C:FD8202 2.4 1.0 1.0
C20 C:FD8202 2.5 0.6 1.0
F6 C:FD8202 2.8 0.6 1.0
F8 C:FD8202 2.8 0.8 1.0
NH1 D:ARG109 3.5 73.4 1.0
CD2 D:TYR107 3.6 68.1 1.0
C17 C:FD8202 3.7 0.6 1.0
C15 C:FD8202 3.7 0.7 1.0
CB D:TYR107 4.0 66.5 1.0
CG D:TYR107 4.1 67.1 1.0
C16 C:FD8202 4.2 0.2 1.0
CA D:TYR107 4.2 65.1 1.0
CZ D:ARG109 4.4 70.9 1.0
CE2 D:TYR107 4.4 68.7 1.0
NE D:ARG109 4.4 68.7 1.0
O D:TYR107 4.7 65.5 1.0
O2 C:FD8202 4.8 0.3 1.0
F5 C:FD8202 4.8 0.6 1.0
O D:ASP106 4.9 64.7 1.0
C D:TYR107 5.0 66.9 1.0

Fluorine binding site 8 out of 16 in 4ytn

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Fluorine binding site 8 out of 16 in the Crystal Structure of Mitochondrial Rhodoquinol-Fumarate Reductase From Ascaris Suum with N-[3-(Pentafluorophenoxy)Phenyl]-2- (Trifluoromethyl)Benzamide


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 8 of Crystal Structure of Mitochondrial Rhodoquinol-Fumarate Reductase From Ascaris Suum with N-[3-(Pentafluorophenoxy)Phenyl]-2- (Trifluoromethyl)Benzamide within 5.0Å range:
probe atom residue distance (Å) B Occ
C:F202

b:0.8
occ:1.00
 F8 C:FD8202 0.0 0.8 1.0
C20 C:FD8202 1.3 0.6 1.0
C15 C:FD8202 2.3 0.7 1.0
C19 C:FD8202 2.4 0.4 1.0
O2 C:FD8202 2.7 0.3 1.0
CD2 D:TYR107 2.8 68.1 1.0
F7 C:FD8202 2.8 0.6 1.0
CE2 D:TYR107 2.8 68.7 1.0
CG D:TYR107 3.3 67.1 1.0
CZ D:TYR107 3.4 68.4 1.0
C13 C:FD8202 3.4 0.9 1.0
C14 C:FD8202 3.5 0.9 1.0
C16 C:FD8202 3.6 0.2 1.0
C18 C:FD8202 3.7 1.0 1.0
CD1 D:TYR107 3.8 66.8 1.0
CE1 D:TYR107 3.8 67.4 1.0
C17 C:FD8202 4.1 0.6 1.0
CB D:TYR107 4.2 66.5 1.0
OH D:TYR107 4.2 69.6 1.0
C12 C:FD8202 4.7 0.6 1.0
F4 C:FD8202 4.8 0.9 1.0
C9 C:FD8202 4.8 0.9 1.0
F6 C:FD8202 4.8 0.6 1.0

Fluorine binding site 9 out of 16 in 4ytn

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Fluorine binding site 9 out of 16 in the Crystal Structure of Mitochondrial Rhodoquinol-Fumarate Reductase From Ascaris Suum with N-[3-(Pentafluorophenoxy)Phenyl]-2- (Trifluoromethyl)Benzamide


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 9 of Crystal Structure of Mitochondrial Rhodoquinol-Fumarate Reductase From Ascaris Suum with N-[3-(Pentafluorophenoxy)Phenyl]-2- (Trifluoromethyl)Benzamide within 5.0Å range:
probe atom residue distance (Å) B Occ
F:F304

b:0.2
occ:1.00
 F1 F:FD8304 0.0 0.2 1.0
C1 F:FD8304 1.3 0.9 1.0
F2 F:FD8304 2.1 0.7 1.0
F3 F:FD8304 2.2 0.1 1.0
C2 F:FD8304 2.2 0.4 1.0
O1 F:FD8304 2.5 0.5 1.0
NE1 F:TRP197 2.5 56.0 1.0
C3 F:FD8304 2.8 0.5 1.0
C8 F:FD8304 2.8 0.8 1.0
CD1 F:TRP197 2.9 55.0 1.0
CB F:PRO193 3.4 56.7 1.0
C7 F:FD8304 3.4 0.4 1.0
C F:PRO193 3.6 55.8 1.0
N F:SER194 3.7 56.0 1.0
CE2 F:TRP197 3.8 55.3 1.0
O F:PRO193 3.8 53.2 1.0
N F:FD8304 4.0 0.1 1.0
CA F:SER194 4.0 59.4 1.0
CA F:PRO193 4.1 56.1 1.0
C4 F:FD8304 4.2 0.9 1.0
CG F:TRP197 4.2 55.7 1.0
NH1 G:ARG76 4.5 67.9 1.0
CZ2 F:TRP197 4.6 53.6 1.0
C6 F:FD8304 4.6 0.6 1.0
CG F:PRO193 4.6 57.2 1.0
CD2 F:TRP197 4.6 54.6 1.0
OH H:TYR107 4.7 84.2 1.0
CD1 F:ILE242 4.7 64.0 1.0
CE2 H:TYR107 4.7 82.4 1.0
C9 F:FD8304 4.7 0.7 1.0
CB F:SER194 4.8 60.4 1.0
OD1 H:ASP106 4.8 66.0 1.0
CG H:ASP106 4.9 63.6 1.0
C5 F:FD8304 4.9 99.4 1.0

Fluorine binding site 10 out of 16 in 4ytn

Go back to Fluorine Binding Sites List in 4ytn
Fluorine binding site 10 out of 16 in the Crystal Structure of Mitochondrial Rhodoquinol-Fumarate Reductase From Ascaris Suum with N-[3-(Pentafluorophenoxy)Phenyl]-2- (Trifluoromethyl)Benzamide


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 10 of Crystal Structure of Mitochondrial Rhodoquinol-Fumarate Reductase From Ascaris Suum with N-[3-(Pentafluorophenoxy)Phenyl]-2- (Trifluoromethyl)Benzamide within 5.0Å range:
probe atom residue distance (Å) B Occ
F:F304

b:0.7
occ:1.00
 F2 F:FD8304 0.0 0.7 1.0
C1 F:FD8304 1.3 0.9 1.0
F1 F:FD8304 2.1 0.2 1.0
F3 F:FD8304 2.2 0.1 1.0
C2 F:FD8304 2.3 0.4 1.0
NH1 G:ARG76 2.5 67.9 1.0
O1 F:FD8304 2.9 0.5 1.0
C3 F:FD8304 3.1 0.5 1.0
C7 F:FD8304 3.2 0.4 1.0
CG H:ASP106 3.3 63.6 1.0
OD2 H:ASP106 3.3 64.9 1.0
C8 F:FD8304 3.4 0.8 1.0
CZ G:ARG76 3.5 68.0 1.0
CB H:ASP106 3.6 63.1 1.0
CD1 F:TRP197 3.7 55.0 1.0
OH H:TYR107 3.7 84.2 1.0
OD1 H:ASP106 3.7 66.0 1.0
NE1 F:TRP197 3.7 56.0 1.0
CE2 H:TYR107 3.9 82.4 1.0
NH2 G:ARG76 3.9 69.4 1.0
CZ H:TYR107 4.0 85.3 1.0
C4 F:FD8304 4.4 0.9 1.0
C6 F:FD8304 4.4 0.6 1.0
NE G:ARG76 4.5 66.8 1.0
CD2 F:HIS240 4.7 66.3 1.0
N F:FD8304 4.8 0.1 1.0
CD G:ARG76 4.8 65.3 1.0
CD2 H:TYR107 4.9 78.5 1.0
C5 F:FD8304 4.9 99.4 1.0
CA H:ASP106 5.0 62.1 1.0
CG F:TRP197 5.0 55.7 1.0

Reference:

S.Harada, T.Shiba, D.Sato, A.Yamamoto, M.Nagahama, A.Yone, D.K.Inaoka, K.Sakamoto, M.Inoue, T.Honma, K.Kita. New Insights Into the Design of Inhibitors Targeted For Parasitic Anaerobic Energy Metabolism To Be Published.
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