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Fluorine in PDB 4g7g: Sterol 14-Alpha Demethylase (CYP51) From Trypanosoma Brucei in Complex with the Vni Derivative (R)-N-(1-(3,4'-Difluorobiphenyl-4-Yl)-2-(1H- Imidazol-1-Yl)Ethyl)-4-(5-Phenyl-1,3,4-Oxadiazol-2-Yl)Benzamide [Vni/Vnf (Vfv)]

Enzymatic activity of Sterol 14-Alpha Demethylase (CYP51) From Trypanosoma Brucei in Complex with the Vni Derivative (R)-N-(1-(3,4'-Difluorobiphenyl-4-Yl)-2-(1H- Imidazol-1-Yl)Ethyl)-4-(5-Phenyl-1,3,4-Oxadiazol-2-Yl)Benzamide [Vni/Vnf (Vfv)]

All present enzymatic activity of Sterol 14-Alpha Demethylase (CYP51) From Trypanosoma Brucei in Complex with the Vni Derivative (R)-N-(1-(3,4'-Difluorobiphenyl-4-Yl)-2-(1H- Imidazol-1-Yl)Ethyl)-4-(5-Phenyl-1,3,4-Oxadiazol-2-Yl)Benzamide [Vni/Vnf (Vfv)]:
1.14.13.70;

Protein crystallography data

The structure of Sterol 14-Alpha Demethylase (CYP51) From Trypanosoma Brucei in Complex with the Vni Derivative (R)-N-(1-(3,4'-Difluorobiphenyl-4-Yl)-2-(1H- Imidazol-1-Yl)Ethyl)-4-(5-Phenyl-1,3,4-Oxadiazol-2-Yl)Benzamide [Vni/Vnf (Vfv)], PDB code: 4g7g was solved by T.Y.Hargrove, Z.Wawrzak, M.R.Waterman, G.I.Lepesheva, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 29.82 / 2.05
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 59.947, 79.706, 117.868, 74.64, 81.20, 68.96
R / Rfree (%) 16.3 / 22.6

Other elements in 4g7g:

The structure of Sterol 14-Alpha Demethylase (CYP51) From Trypanosoma Brucei in Complex with the Vni Derivative (R)-N-(1-(3,4'-Difluorobiphenyl-4-Yl)-2-(1H- Imidazol-1-Yl)Ethyl)-4-(5-Phenyl-1,3,4-Oxadiazol-2-Yl)Benzamide [Vni/Vnf (Vfv)] also contains other interesting chemical elements:

Iron (Fe) 4 atoms

Fluorine Binding Sites:

The binding sites of Fluorine atom in the Sterol 14-Alpha Demethylase (CYP51) From Trypanosoma Brucei in Complex with the Vni Derivative (R)-N-(1-(3,4'-Difluorobiphenyl-4-Yl)-2-(1H- Imidazol-1-Yl)Ethyl)-4-(5-Phenyl-1,3,4-Oxadiazol-2-Yl)Benzamide [Vni/Vnf (Vfv)] (pdb code 4g7g). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 8 binding sites of Fluorine where determined in the Sterol 14-Alpha Demethylase (CYP51) From Trypanosoma Brucei in Complex with the Vni Derivative (R)-N-(1-(3,4'-Difluorobiphenyl-4-Yl)-2-(1H- Imidazol-1-Yl)Ethyl)-4-(5-Phenyl-1,3,4-Oxadiazol-2-Yl)Benzamide [Vni/Vnf (Vfv)], PDB code: 4g7g:
Jump to Fluorine binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Fluorine binding site 1 out of 8 in 4g7g

Go back to Fluorine Binding Sites List in 4g7g
Fluorine binding site 1 out of 8 in the Sterol 14-Alpha Demethylase (CYP51) From Trypanosoma Brucei in Complex with the Vni Derivative (R)-N-(1-(3,4'-Difluorobiphenyl-4-Yl)-2-(1H- Imidazol-1-Yl)Ethyl)-4-(5-Phenyl-1,3,4-Oxadiazol-2-Yl)Benzamide [Vni/Vnf (Vfv)]


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of Sterol 14-Alpha Demethylase (CYP51) From Trypanosoma Brucei in Complex with the Vni Derivative (R)-N-(1-(3,4'-Difluorobiphenyl-4-Yl)-2-(1H- Imidazol-1-Yl)Ethyl)-4-(5-Phenyl-1,3,4-Oxadiazol-2-Yl)Benzamide [Vni/Vnf (Vfv)] within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F502

b:43.3
occ:1.00
 FAB A:VFV502 0.0 43.3 1.0
CBD A:VFV502 1.4 42.1 1.0
CAK A:VFV502 2.4 40.5 1.0
CAJ A:VFV502 2.4 37.0 1.0
CD2 A:LEU127 3.2 38.0 1.0
CE A:MET284 3.6 39.7 1.0
CAO A:VFV502 3.7 39.6 1.0
CB A:ALA115 3.7 33.7 1.0
CAN A:VFV502 3.7 38.0 1.0
CG A:LEU127 3.7 42.0 1.0
CA A:ALA115 3.8 35.0 1.0
SD A:MET284 3.8 38.0 1.0
CBG A:VFV502 4.2 35.6 1.0
CG A:MET123 4.3 45.5 1.0
N A:ALA115 4.6 32.2 1.0
CD1 A:LEU127 4.7 45.0 1.0
SD A:MET123 4.7 50.9 1.0
N A:LEU127 4.7 34.7 1.0
CMD A:HEM501 4.8 26.7 1.0
CA A:LEU127 4.8 39.6 1.0
CB A:LEU127 4.8 39.3 1.0
OE1 A:GLN126 4.9 35.3 1.0
O A:MET123 4.9 35.0 1.0
C A:ALA115 5.0 33.1 1.0
CB A:GLN126 5.0 37.3 1.0

Fluorine binding site 2 out of 8 in 4g7g

Go back to Fluorine Binding Sites List in 4g7g
Fluorine binding site 2 out of 8 in the Sterol 14-Alpha Demethylase (CYP51) From Trypanosoma Brucei in Complex with the Vni Derivative (R)-N-(1-(3,4'-Difluorobiphenyl-4-Yl)-2-(1H- Imidazol-1-Yl)Ethyl)-4-(5-Phenyl-1,3,4-Oxadiazol-2-Yl)Benzamide [Vni/Vnf (Vfv)]


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of Sterol 14-Alpha Demethylase (CYP51) From Trypanosoma Brucei in Complex with the Vni Derivative (R)-N-(1-(3,4'-Difluorobiphenyl-4-Yl)-2-(1H- Imidazol-1-Yl)Ethyl)-4-(5-Phenyl-1,3,4-Oxadiazol-2-Yl)Benzamide [Vni/Vnf (Vfv)] within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F502

b:28.3
occ:1.00
 FAC A:VFV502 0.0 28.3 1.0
CBE A:VFV502 1.3 27.8 1.0
CBK A:VFV502 2.3 27.2 1.0
CAV A:VFV502 2.3 24.0 1.0
CBN A:VFV502 2.7 27.3 1.0
N A:ALA291 3.4 28.6 1.0
CA A:ALA291 3.5 27.6 1.0
C A:PHE290 3.6 36.5 1.0
CBJ A:VFV502 3.6 30.5 1.0
CAS A:VFV502 3.6 28.9 1.0
NBA A:VFV502 3.6 27.0 1.0
CB A:PHE290 3.6 37.8 1.0
O A:HOH750 3.7 43.8 1.0
O A:PHE290 3.8 33.5 1.0
CB A:ALA291 4.0 24.7 1.0
O A:ALA287 4.0 31.5 1.0
CAW A:VFV502 4.0 25.2 1.0
CAR A:VFV502 4.1 27.8 1.0
OAA A:VFV502 4.2 34.7 1.0
CBC A:VFV502 4.2 31.4 1.0
CA A:PHE290 4.3 35.5 1.0
CE A:MET106 4.3 45.3 1.0
NBO A:VFV502 4.4 26.6 1.0
CAT A:VFV502 4.5 21.8 1.0
CG A:PHE290 4.7 39.4 1.0
CBG A:VFV502 4.8 35.6 1.0
CD2 A:PHE290 4.8 41.7 1.0
C A:ALA291 4.9 29.7 1.0
SD A:MET106 5.0 36.9 1.0

Fluorine binding site 3 out of 8 in 4g7g

Go back to Fluorine Binding Sites List in 4g7g
Fluorine binding site 3 out of 8 in the Sterol 14-Alpha Demethylase (CYP51) From Trypanosoma Brucei in Complex with the Vni Derivative (R)-N-(1-(3,4'-Difluorobiphenyl-4-Yl)-2-(1H- Imidazol-1-Yl)Ethyl)-4-(5-Phenyl-1,3,4-Oxadiazol-2-Yl)Benzamide [Vni/Vnf (Vfv)]


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of Sterol 14-Alpha Demethylase (CYP51) From Trypanosoma Brucei in Complex with the Vni Derivative (R)-N-(1-(3,4'-Difluorobiphenyl-4-Yl)-2-(1H- Imidazol-1-Yl)Ethyl)-4-(5-Phenyl-1,3,4-Oxadiazol-2-Yl)Benzamide [Vni/Vnf (Vfv)] within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F502

b:65.7
occ:1.00
 FAB B:VFV502 0.0 65.7 1.0
CBD B:VFV502 1.4 43.8 1.0
CAK B:VFV502 2.4 42.2 1.0
CAJ B:VFV502 2.4 43.4 1.0
CE B:MET284 3.0 50.0 1.0
SD B:MET284 3.4 42.5 1.0
CD2 B:LEU127 3.4 37.2 1.0
CAO B:VFV502 3.6 37.8 1.0
CAN B:VFV502 3.6 38.3 1.0
CB B:ALA115 4.1 31.9 1.0
CBG B:VFV502 4.1 32.2 1.0
CG B:LEU127 4.2 39.0 1.0
CMD B:HEM501 4.5 31.0 1.0
CA B:ALA115 4.5 34.5 1.0
CD2 B:LEU130 4.5 28.4 1.0
N B:LEU127 4.8 30.9 1.0
CA B:LEU127 4.8 28.5 1.0
CB B:GLN126 5.0 28.3 1.0

Fluorine binding site 4 out of 8 in 4g7g

Go back to Fluorine Binding Sites List in 4g7g
Fluorine binding site 4 out of 8 in the Sterol 14-Alpha Demethylase (CYP51) From Trypanosoma Brucei in Complex with the Vni Derivative (R)-N-(1-(3,4'-Difluorobiphenyl-4-Yl)-2-(1H- Imidazol-1-Yl)Ethyl)-4-(5-Phenyl-1,3,4-Oxadiazol-2-Yl)Benzamide [Vni/Vnf (Vfv)]


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 4 of Sterol 14-Alpha Demethylase (CYP51) From Trypanosoma Brucei in Complex with the Vni Derivative (R)-N-(1-(3,4'-Difluorobiphenyl-4-Yl)-2-(1H- Imidazol-1-Yl)Ethyl)-4-(5-Phenyl-1,3,4-Oxadiazol-2-Yl)Benzamide [Vni/Vnf (Vfv)] within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F502

b:28.3
occ:1.00
 FAC B:VFV502 0.0 28.3 1.0
CBE B:VFV502 1.4 27.9 1.0
CBK B:VFV502 2.4 25.2 1.0
CAV B:VFV502 2.4 26.5 1.0
CBN B:VFV502 2.8 25.7 1.0
CA B:ALA291 3.3 28.5 1.0
N B:ALA291 3.3 33.5 1.0
O B:HOH622 3.4 49.3 1.0
CB B:ALA291 3.5 27.1 1.0
CD1 B:PHE290 3.6 46.3 1.0
CBJ B:VFV502 3.6 27.9 1.0
CAS B:VFV502 3.7 26.8 1.0
O B:ALA287 3.7 27.1 1.0
NBA B:VFV502 3.8 26.9 1.0
CB B:PHE290 4.0 46.6 1.0
CAW B:VFV502 4.1 23.2 1.0
C B:PHE290 4.1 42.9 1.0
OAA B:VFV502 4.1 33.9 1.0
CAR B:VFV502 4.2 32.4 1.0
CE B:MET106 4.2 40.4 1.0
CG B:PHE290 4.2 52.1 1.0
CBC B:VFV502 4.3 30.0 1.0
NBO B:VFV502 4.3 25.1 1.0
CE1 B:PHE290 4.5 51.2 1.0
CAT B:VFV502 4.5 25.6 1.0
O B:PHE290 4.7 46.2 1.0
CA B:PHE290 4.7 40.9 1.0
C B:ALA291 4.8 25.6 1.0
C B:ALA287 4.8 27.2 1.0
CBG B:VFV502 4.8 32.2 1.0

Fluorine binding site 5 out of 8 in 4g7g

Go back to Fluorine Binding Sites List in 4g7g
Fluorine binding site 5 out of 8 in the Sterol 14-Alpha Demethylase (CYP51) From Trypanosoma Brucei in Complex with the Vni Derivative (R)-N-(1-(3,4'-Difluorobiphenyl-4-Yl)-2-(1H- Imidazol-1-Yl)Ethyl)-4-(5-Phenyl-1,3,4-Oxadiazol-2-Yl)Benzamide [Vni/Vnf (Vfv)]


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 5 of Sterol 14-Alpha Demethylase (CYP51) From Trypanosoma Brucei in Complex with the Vni Derivative (R)-N-(1-(3,4'-Difluorobiphenyl-4-Yl)-2-(1H- Imidazol-1-Yl)Ethyl)-4-(5-Phenyl-1,3,4-Oxadiazol-2-Yl)Benzamide [Vni/Vnf (Vfv)] within 5.0Å range:
probe atom residue distance (Å) B Occ
C:F502

b:68.8
occ:1.00
 FAB C:VFV502 0.0 68.8 1.0
CBD C:VFV502 1.3 58.1 1.0
CAJ C:VFV502 2.3 67.0 1.0
CAK C:VFV502 2.3 59.0 1.0
CE C:MET284 3.1 54.9 1.0
SD C:MET284 3.5 60.5 1.0
CAN C:VFV502 3.6 59.9 1.0
CAO C:VFV502 3.6 57.6 1.0
CD2 C:LEU127 3.6 46.7 1.0
CD2 C:LEU130 4.0 40.7 1.0
CBG C:VFV502 4.1 53.8 1.0
CB C:ALA115 4.2 38.0 1.0
CG C:LEU127 4.5 55.6 1.0
CMD C:HEM501 4.6 42.1 1.0
CB C:ALA287 4.7 49.6 1.0
CA C:ALA115 4.7 45.1 1.0

Fluorine binding site 6 out of 8 in 4g7g

Go back to Fluorine Binding Sites List in 4g7g
Fluorine binding site 6 out of 8 in the Sterol 14-Alpha Demethylase (CYP51) From Trypanosoma Brucei in Complex with the Vni Derivative (R)-N-(1-(3,4'-Difluorobiphenyl-4-Yl)-2-(1H- Imidazol-1-Yl)Ethyl)-4-(5-Phenyl-1,3,4-Oxadiazol-2-Yl)Benzamide [Vni/Vnf (Vfv)]


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 6 of Sterol 14-Alpha Demethylase (CYP51) From Trypanosoma Brucei in Complex with the Vni Derivative (R)-N-(1-(3,4'-Difluorobiphenyl-4-Yl)-2-(1H- Imidazol-1-Yl)Ethyl)-4-(5-Phenyl-1,3,4-Oxadiazol-2-Yl)Benzamide [Vni/Vnf (Vfv)] within 5.0Å range:
probe atom residue distance (Å) B Occ
C:F502

b:41.8
occ:1.00
 FAC C:VFV502 0.0 41.8 1.0
CBE C:VFV502 1.3 43.6 1.0
CAV C:VFV502 2.3 39.5 1.0
CBK C:VFV502 2.3 36.1 1.0
CBN C:VFV502 2.7 31.4 1.0
NBA C:VFV502 3.5 31.9 1.0
CBJ C:VFV502 3.5 45.0 1.0
CAS C:VFV502 3.6 38.3 1.0
O C:HOH606 3.6 47.7 1.0
N C:ALA291 3.6 35.0 1.0
CA C:ALA291 3.7 36.0 1.0
CB C:PHE290 3.8 49.0 1.0
C C:PHE290 3.9 45.6 1.0
OAA C:VFV502 4.0 35.6 1.0
CBC C:VFV502 4.0 36.0 1.0
CE C:MET106 4.0 41.9 1.0
CAR C:VFV502 4.0 40.3 1.0
CAW C:VFV502 4.1 26.2 1.0
CB C:ALA291 4.1 34.0 1.0
O C:ALA287 4.2 40.3 1.0
O C:PHE290 4.3 43.4 1.0
SD C:MET106 4.4 40.5 1.0
NBO C:VFV502 4.4 25.0 1.0
CA C:PHE290 4.5 42.8 1.0
CAT C:VFV502 4.5 25.6 1.0
CG C:PHE290 4.6 53.5 1.0
CD1 C:PHE290 4.6 56.0 1.0
CBG C:VFV502 4.7 53.8 1.0
CAN C:VFV502 4.9 59.9 1.0
CE2 C:TYR103 5.0 42.8 1.0
CZ C:PHE110 5.0 54.0 1.0

Fluorine binding site 7 out of 8 in 4g7g

Go back to Fluorine Binding Sites List in 4g7g
Fluorine binding site 7 out of 8 in the Sterol 14-Alpha Demethylase (CYP51) From Trypanosoma Brucei in Complex with the Vni Derivative (R)-N-(1-(3,4'-Difluorobiphenyl-4-Yl)-2-(1H- Imidazol-1-Yl)Ethyl)-4-(5-Phenyl-1,3,4-Oxadiazol-2-Yl)Benzamide [Vni/Vnf (Vfv)]


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 7 of Sterol 14-Alpha Demethylase (CYP51) From Trypanosoma Brucei in Complex with the Vni Derivative (R)-N-(1-(3,4'-Difluorobiphenyl-4-Yl)-2-(1H- Imidazol-1-Yl)Ethyl)-4-(5-Phenyl-1,3,4-Oxadiazol-2-Yl)Benzamide [Vni/Vnf (Vfv)] within 5.0Å range:
probe atom residue distance (Å) B Occ
D:F502

b:60.3
occ:1.00
 FAB D:VFV502 0.0 60.3 1.0
CBD D:VFV502 0.9 45.0 1.0
CAJ D:VFV502 1.9 43.0 1.0
CAK D:VFV502 2.0 48.5 1.0
CAN D:VFV502 3.1 45.9 1.0
CAO D:VFV502 3.2 38.4 1.0
CB D:ALA115 3.6 37.8 1.0
CE D:MET284 3.6 55.5 1.0
CBG D:VFV502 3.6 38.0 1.0
CD2 D:LEU127 3.6 48.4 1.0
SD D:MET284 3.8 50.8 1.0
CA D:ALA115 4.0 36.5 1.0
CG D:LEU127 4.2 52.7 1.0
CMD D:HEM501 4.3 34.0 1.0
CB D:ALA287 4.7 30.0 1.0
N D:ALA115 4.9 36.0 1.0
CG D:MET123 4.9 48.7 1.0
CBJ D:VFV502 5.0 33.2 1.0
CD2 D:LEU130 5.0 37.7 1.0

Fluorine binding site 8 out of 8 in 4g7g

Go back to Fluorine Binding Sites List in 4g7g
Fluorine binding site 8 out of 8 in the Sterol 14-Alpha Demethylase (CYP51) From Trypanosoma Brucei in Complex with the Vni Derivative (R)-N-(1-(3,4'-Difluorobiphenyl-4-Yl)-2-(1H- Imidazol-1-Yl)Ethyl)-4-(5-Phenyl-1,3,4-Oxadiazol-2-Yl)Benzamide [Vni/Vnf (Vfv)]


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 8 of Sterol 14-Alpha Demethylase (CYP51) From Trypanosoma Brucei in Complex with the Vni Derivative (R)-N-(1-(3,4'-Difluorobiphenyl-4-Yl)-2-(1H- Imidazol-1-Yl)Ethyl)-4-(5-Phenyl-1,3,4-Oxadiazol-2-Yl)Benzamide [Vni/Vnf (Vfv)] within 5.0Å range:
probe atom residue distance (Å) B Occ
D:F502

b:29.8
occ:1.00
 FAC D:VFV502 0.0 29.8 1.0
CBE D:VFV502 1.2 29.5 1.0
CAV D:VFV502 2.2 26.8 1.0
CBK D:VFV502 2.3 28.8 1.0
CBN D:VFV502 2.7 28.8 1.0
CBJ D:VFV502 3.4 33.2 1.0
N D:ALA291 3.5 33.1 1.0
CAS D:VFV502 3.5 32.9 1.0
CA D:ALA291 3.5 32.7 1.0
NBA D:VFV502 3.6 31.6 1.0
CB D:ALA291 3.8 34.5 1.0
CB D:PHE290 3.8 45.5 1.0
CAW D:VFV502 3.9 24.3 1.0
CAR D:VFV502 3.9 33.5 1.0
C D:PHE290 4.0 43.0 1.0
O D:HOH664 4.0 54.7 1.0
O D:ALA287 4.1 30.2 1.0
OAA D:VFV502 4.2 36.6 1.0
NBO D:VFV502 4.2 30.2 1.0
CBC D:VFV502 4.3 37.4 1.0
CE D:MET106 4.3 38.1 1.0
CAT D:VFV502 4.3 35.3 1.0
O D:PHE290 4.5 45.9 1.0
CBG D:VFV502 4.6 38.0 1.0
CA D:PHE290 4.6 42.8 1.0
CG D:PHE290 4.8 47.5 1.0
CAN D:VFV502 4.9 45.9 1.0
CD1 D:PHE290 4.9 53.8 1.0
C D:ALA291 5.0 29.5 1.0
SD D:MET106 5.0 36.4 1.0
CZ D:PHE110 5.0 50.7 1.0
CAU D:VFV502 5.0 28.1 1.0

Reference:

G.I.Lepesheva, T.Y.Hargrove, G.Rachakonda, Z.Wawrzak, S.Pomel, S.Cojean, P.N.Nde, W.D.Nes, C.W.Locuson, M.W.Calcutt, M.R.Waterman, J.S.Daniels, P.M.Loiseau, F.Villalta. Vfv As A New Effective CYP51 Structure-Derived Drug Candidate For Chagas Disease and Visceral Leishmaniasis. J Infect Dis V. 212 1439 2015.
ISSN: ISSN 1537-6613
PubMed: 25883390
DOI: 10.1093/INFDIS/JIV228
Page generated: Sun Dec 13 12:03:08 2020

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