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Fluorine in PDB 6cr2: Crystal Structure of Sterol 14-Alpha Demethylase (CYP51B) From Aspergillus Fumigatus in Complex with the Vni Derivative N-(1-(2,4- Dichlorophenyl)-2-(1H-Imidazol-1-Yl)Ethyl)-4-(5-(2-Fluoro-4-(2,2,2- Trifluoroethoxy)Phenyl)-1,3,4-Oxadiazol-2-Yl)Benzamide

Enzymatic activity of Crystal Structure of Sterol 14-Alpha Demethylase (CYP51B) From Aspergillus Fumigatus in Complex with the Vni Derivative N-(1-(2,4- Dichlorophenyl)-2-(1H-Imidazol-1-Yl)Ethyl)-4-(5-(2-Fluoro-4-(2,2,2- Trifluoroethoxy)Phenyl)-1,3,4-Oxadiazol-2-Yl)Benzamide

All present enzymatic activity of Crystal Structure of Sterol 14-Alpha Demethylase (CYP51B) From Aspergillus Fumigatus in Complex with the Vni Derivative N-(1-(2,4- Dichlorophenyl)-2-(1H-Imidazol-1-Yl)Ethyl)-4-(5-(2-Fluoro-4-(2,2,2- Trifluoroethoxy)Phenyl)-1,3,4-Oxadiazol-2-Yl)Benzamide:
1.14.13.70;

Protein crystallography data

The structure of Crystal Structure of Sterol 14-Alpha Demethylase (CYP51B) From Aspergillus Fumigatus in Complex with the Vni Derivative N-(1-(2,4- Dichlorophenyl)-2-(1H-Imidazol-1-Yl)Ethyl)-4-(5-(2-Fluoro-4-(2,2,2- Trifluoroethoxy)Phenyl)-1,3,4-Oxadiazol-2-Yl)Benzamide, PDB code: 6cr2 was solved by L.Friggeri, T.Y.Hargrove, Z.Wawrzak, G.I.Lepesheva, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 30.00 / 2.38
Space group P 31
Cell size a, b, c (Å), α, β, γ (°) 108.438, 108.438, 90.999, 90.00, 90.00, 120.00
R / Rfree (%) 21.5 / 23

Other elements in 6cr2:

The structure of Crystal Structure of Sterol 14-Alpha Demethylase (CYP51B) From Aspergillus Fumigatus in Complex with the Vni Derivative N-(1-(2,4- Dichlorophenyl)-2-(1H-Imidazol-1-Yl)Ethyl)-4-(5-(2-Fluoro-4-(2,2,2- Trifluoroethoxy)Phenyl)-1,3,4-Oxadiazol-2-Yl)Benzamide also contains other interesting chemical elements:

Iron (Fe) 2 atoms
Chlorine (Cl) 4 atoms

Fluorine Binding Sites:

The binding sites of Fluorine atom in the Crystal Structure of Sterol 14-Alpha Demethylase (CYP51B) From Aspergillus Fumigatus in Complex with the Vni Derivative N-(1-(2,4- Dichlorophenyl)-2-(1H-Imidazol-1-Yl)Ethyl)-4-(5-(2-Fluoro-4-(2,2,2- Trifluoroethoxy)Phenyl)-1,3,4-Oxadiazol-2-Yl)Benzamide (pdb code 6cr2). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 8 binding sites of Fluorine where determined in the Crystal Structure of Sterol 14-Alpha Demethylase (CYP51B) From Aspergillus Fumigatus in Complex with the Vni Derivative N-(1-(2,4- Dichlorophenyl)-2-(1H-Imidazol-1-Yl)Ethyl)-4-(5-(2-Fluoro-4-(2,2,2- Trifluoroethoxy)Phenyl)-1,3,4-Oxadiazol-2-Yl)Benzamide, PDB code: 6cr2:
Jump to Fluorine binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Fluorine binding site 1 out of 8 in 6cr2

Go back to Fluorine Binding Sites List in 6cr2
Fluorine binding site 1 out of 8 in the Crystal Structure of Sterol 14-Alpha Demethylase (CYP51B) From Aspergillus Fumigatus in Complex with the Vni Derivative N-(1-(2,4- Dichlorophenyl)-2-(1H-Imidazol-1-Yl)Ethyl)-4-(5-(2-Fluoro-4-(2,2,2- Trifluoroethoxy)Phenyl)-1,3,4-Oxadiazol-2-Yl)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 Sterol 14-Alpha Demethylase (CYP51B) From Aspergillus Fumigatus in Complex with the Vni Derivative N-(1-(2,4- Dichlorophenyl)-2-(1H-Imidazol-1-Yl)Ethyl)-4-(5-(2-Fluoro-4-(2,2,2- Trifluoroethoxy)Phenyl)-1,3,4-Oxadiazol-2-Yl)Benzamide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F602

b:0.6
occ:1.00
 FAB A:LFV602 0.0 0.6 1.0
CBE A:LFV602 1.6 0.9 1.0
NAY A:LFV602 2.4 71.6 1.0
CBJ A:LFV602 2.5 0.5 1.0
CAT A:LFV602 2.6 0.1 1.0
CBM A:LFV602 2.8 96.8 1.0
NAX A:LFV602 3.7 80.8 1.0
CAO A:LFV602 3.8 0.4 1.0
OBB A:LFV602 3.9 88.0 1.0
CBF A:LFV602 3.9 0.1 1.0
O A:VAL121 4.2 40.9 1.0
CD1 A:PHE234 4.3 87.3 1.0
CAJ A:LFV602 4.3 0.1 1.0
CG1 A:VAL121 4.4 44.2 1.0
CBL A:LFV602 4.4 85.6 1.0
O A:PHE234 4.5 53.9 1.0
CB A:PHE234 4.6 71.1 1.0
CG A:PHE234 4.6 80.6 1.0
CA A:PHE234 4.7 61.8 1.0
CE1 A:PHE234 4.9 93.9 1.0

Fluorine binding site 2 out of 8 in 6cr2

Go back to Fluorine Binding Sites List in 6cr2
Fluorine binding site 2 out of 8 in the Crystal Structure of Sterol 14-Alpha Demethylase (CYP51B) From Aspergillus Fumigatus in Complex with the Vni Derivative N-(1-(2,4- Dichlorophenyl)-2-(1H-Imidazol-1-Yl)Ethyl)-4-(5-(2-Fluoro-4-(2,2,2- Trifluoroethoxy)Phenyl)-1,3,4-Oxadiazol-2-Yl)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 Sterol 14-Alpha Demethylase (CYP51B) From Aspergillus Fumigatus in Complex with the Vni Derivative N-(1-(2,4- Dichlorophenyl)-2-(1H-Imidazol-1-Yl)Ethyl)-4-(5-(2-Fluoro-4-(2,2,2- Trifluoroethoxy)Phenyl)-1,3,4-Oxadiazol-2-Yl)Benzamide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F602

b:93.8
occ:1.00
 FAE A:LFV602 0.0 93.8 1.0
CBP A:LFV602 1.1 99.6 1.0
FAD A:LFV602 1.9 79.9 1.0
FAC A:LFV602 1.9 90.7 1.0
CAU A:LFV602 2.1 0.7 1.0
OBA A:LFV602 2.9 1.0 1.0
CD2 A:PHE234 3.3 91.5 1.0
CE2 A:PHE234 3.6 93.2 1.0
CBF A:LFV602 3.8 0.1 1.0
CAJ A:LFV602 4.1 0.1 1.0
CG A:PHE234 4.4 80.6 1.0
CD1 A:LEU92 4.7 60.2 1.0
CB A:PHE234 4.9 71.1 1.0
CZ A:PHE234 4.9 97.7 1.0

Fluorine binding site 3 out of 8 in 6cr2

Go back to Fluorine Binding Sites List in 6cr2
Fluorine binding site 3 out of 8 in the Crystal Structure of Sterol 14-Alpha Demethylase (CYP51B) From Aspergillus Fumigatus in Complex with the Vni Derivative N-(1-(2,4- Dichlorophenyl)-2-(1H-Imidazol-1-Yl)Ethyl)-4-(5-(2-Fluoro-4-(2,2,2- Trifluoroethoxy)Phenyl)-1,3,4-Oxadiazol-2-Yl)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 Sterol 14-Alpha Demethylase (CYP51B) From Aspergillus Fumigatus in Complex with the Vni Derivative N-(1-(2,4- Dichlorophenyl)-2-(1H-Imidazol-1-Yl)Ethyl)-4-(5-(2-Fluoro-4-(2,2,2- Trifluoroethoxy)Phenyl)-1,3,4-Oxadiazol-2-Yl)Benzamide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F602

b:90.7
occ:1.00
 FAC A:LFV602 0.0 90.7 1.0
CBP A:LFV602 1.2 99.6 1.0
FAE A:LFV602 1.9 93.8 1.0
FAD A:LFV602 1.9 79.9 1.0
CAU A:LFV602 2.2 0.7 1.0
OBA A:LFV602 3.5 1.0 1.0
CE2 A:TYR68 4.3 36.0 1.0
CAJ A:LFV602 4.4 0.1 1.0
CE2 A:PHE234 4.4 93.2 1.0
CBF A:LFV602 4.4 0.1 1.0
CD2 A:TYR68 4.5 31.8 1.0
CA A:GLY69 4.6 36.2 1.0
CD2 A:PHE234 4.6 91.5 1.0
N A:SER502 4.8 55.5 1.0

Fluorine binding site 4 out of 8 in 6cr2

Go back to Fluorine Binding Sites List in 6cr2
Fluorine binding site 4 out of 8 in the Crystal Structure of Sterol 14-Alpha Demethylase (CYP51B) From Aspergillus Fumigatus in Complex with the Vni Derivative N-(1-(2,4- Dichlorophenyl)-2-(1H-Imidazol-1-Yl)Ethyl)-4-(5-(2-Fluoro-4-(2,2,2- Trifluoroethoxy)Phenyl)-1,3,4-Oxadiazol-2-Yl)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 Sterol 14-Alpha Demethylase (CYP51B) From Aspergillus Fumigatus in Complex with the Vni Derivative N-(1-(2,4- Dichlorophenyl)-2-(1H-Imidazol-1-Yl)Ethyl)-4-(5-(2-Fluoro-4-(2,2,2- Trifluoroethoxy)Phenyl)-1,3,4-Oxadiazol-2-Yl)Benzamide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F602

b:79.9
occ:1.00
 FAD A:LFV602 0.0 79.9 1.0
CBP A:LFV602 1.1 99.6 1.0
FAE A:LFV602 1.9 93.8 1.0
FAC A:LFV602 1.9 90.7 1.0
CAU A:LFV602 2.1 0.7 1.0
OBA A:LFV602 2.8 1.0 1.0
CD1 A:LEU91 3.8 50.5 1.0
CBF A:LFV602 4.2 0.1 1.0
CG2 A:THR65 4.2 52.8 1.0
CD2 A:TYR68 4.2 31.8 1.0
CE2 A:TYR68 4.3 36.0 1.0
CD1 A:LEU92 4.6 60.2 1.0
CAJ A:LFV602 4.7 0.1 1.0
CD2 A:PHE234 4.8 91.5 1.0
CG A:LEU92 4.8 70.9 1.0
CG A:LEU91 4.9 50.7 1.0

Fluorine binding site 5 out of 8 in 6cr2

Go back to Fluorine Binding Sites List in 6cr2
Fluorine binding site 5 out of 8 in the Crystal Structure of Sterol 14-Alpha Demethylase (CYP51B) From Aspergillus Fumigatus in Complex with the Vni Derivative N-(1-(2,4- Dichlorophenyl)-2-(1H-Imidazol-1-Yl)Ethyl)-4-(5-(2-Fluoro-4-(2,2,2- Trifluoroethoxy)Phenyl)-1,3,4-Oxadiazol-2-Yl)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 Sterol 14-Alpha Demethylase (CYP51B) From Aspergillus Fumigatus in Complex with the Vni Derivative N-(1-(2,4- Dichlorophenyl)-2-(1H-Imidazol-1-Yl)Ethyl)-4-(5-(2-Fluoro-4-(2,2,2- Trifluoroethoxy)Phenyl)-1,3,4-Oxadiazol-2-Yl)Benzamide within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F602

b:72.1
occ:1.00
 FAB B:LFV602 0.0 72.1 1.0
CBE B:LFV602 1.4 75.5 1.0
CAT B:LFV602 2.4 66.7 1.0
CBJ B:LFV602 2.4 66.1 1.0
NAY B:LFV602 2.6 55.8 1.0
CBM B:LFV602 2.8 73.0 1.0
CAO B:LFV602 3.7 64.9 1.0
CBF B:LFV602 3.7 64.0 1.0
CD1 B:PHE234 3.8 72.8 1.0
O B:VAL121 3.9 41.7 1.0
NAX B:LFV602 4.0 60.1 1.0
CG1 B:VAL121 4.1 36.3 1.0
CAJ B:LFV602 4.1 70.6 1.0
OBB B:LFV602 4.2 69.8 1.0
O B:PHE234 4.3 54.5 1.0
CE1 B:PHE234 4.4 76.3 1.0
CG B:PHE234 4.6 78.1 1.0
CBL B:LFV602 4.7 59.0 1.0
CB B:PHE234 4.7 61.5 1.0
OBA B:LFV602 4.8 62.6 1.0
C B:VAL121 4.9 38.0 1.0
CA B:PHE234 4.9 51.0 1.0

Fluorine binding site 6 out of 8 in 6cr2

Go back to Fluorine Binding Sites List in 6cr2
Fluorine binding site 6 out of 8 in the Crystal Structure of Sterol 14-Alpha Demethylase (CYP51B) From Aspergillus Fumigatus in Complex with the Vni Derivative N-(1-(2,4- Dichlorophenyl)-2-(1H-Imidazol-1-Yl)Ethyl)-4-(5-(2-Fluoro-4-(2,2,2- Trifluoroethoxy)Phenyl)-1,3,4-Oxadiazol-2-Yl)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 Sterol 14-Alpha Demethylase (CYP51B) From Aspergillus Fumigatus in Complex with the Vni Derivative N-(1-(2,4- Dichlorophenyl)-2-(1H-Imidazol-1-Yl)Ethyl)-4-(5-(2-Fluoro-4-(2,2,2- Trifluoroethoxy)Phenyl)-1,3,4-Oxadiazol-2-Yl)Benzamide within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F602

b:56.1
occ:1.00
 FAE B:LFV602 0.0 56.1 1.0
CBP B:LFV602 1.2 83.4 1.0
FAD B:LFV602 1.9 56.5 1.0
FAC B:LFV602 2.0 67.2 1.0
CAU B:LFV602 2.3 63.5 1.0
OBA B:LFV602 3.5 62.6 1.0
O B:MET235 3.7 45.6 1.0
NE1 B:TRP238 4.2 39.2 1.0
C B:MET235 4.6 44.7 1.0
CBF B:LFV602 4.7 64.0 1.0
CA B:MET235 4.9 52.4 1.0

Fluorine binding site 7 out of 8 in 6cr2

Go back to Fluorine Binding Sites List in 6cr2
Fluorine binding site 7 out of 8 in the Crystal Structure of Sterol 14-Alpha Demethylase (CYP51B) From Aspergillus Fumigatus in Complex with the Vni Derivative N-(1-(2,4- Dichlorophenyl)-2-(1H-Imidazol-1-Yl)Ethyl)-4-(5-(2-Fluoro-4-(2,2,2- Trifluoroethoxy)Phenyl)-1,3,4-Oxadiazol-2-Yl)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 Sterol 14-Alpha Demethylase (CYP51B) From Aspergillus Fumigatus in Complex with the Vni Derivative N-(1-(2,4- Dichlorophenyl)-2-(1H-Imidazol-1-Yl)Ethyl)-4-(5-(2-Fluoro-4-(2,2,2- Trifluoroethoxy)Phenyl)-1,3,4-Oxadiazol-2-Yl)Benzamide within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F602

b:67.2
occ:1.00
 FAC B:LFV602 0.0 67.2 1.0
CBP B:LFV602 1.2 83.4 1.0
FAD B:LFV602 1.9 56.5 1.0
FAE B:LFV602 2.0 56.1 1.0
CAU B:LFV602 2.3 63.5 1.0
OBA B:LFV602 2.6 62.6 1.0
NE1 B:TRP238 3.7 39.2 1.0
CB B:PRO124 3.9 33.6 1.0
CBF B:LFV602 3.9 64.0 1.0
CG B:PRO124 4.1 36.9 1.0
CD1 B:TRP238 4.1 42.3 1.0
CG B:PRO237 4.2 30.3 1.0
CD B:PRO237 4.2 30.1 1.0
O B:MET235 4.2 45.6 1.0
CAJ B:LFV602 4.7 70.6 1.0
CAT B:LFV602 4.8 66.7 1.0
CE2 B:TRP238 5.0 42.7 1.0

Fluorine binding site 8 out of 8 in 6cr2

Go back to Fluorine Binding Sites List in 6cr2
Fluorine binding site 8 out of 8 in the Crystal Structure of Sterol 14-Alpha Demethylase (CYP51B) From Aspergillus Fumigatus in Complex with the Vni Derivative N-(1-(2,4- Dichlorophenyl)-2-(1H-Imidazol-1-Yl)Ethyl)-4-(5-(2-Fluoro-4-(2,2,2- Trifluoroethoxy)Phenyl)-1,3,4-Oxadiazol-2-Yl)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 Sterol 14-Alpha Demethylase (CYP51B) From Aspergillus Fumigatus in Complex with the Vni Derivative N-(1-(2,4- Dichlorophenyl)-2-(1H-Imidazol-1-Yl)Ethyl)-4-(5-(2-Fluoro-4-(2,2,2- Trifluoroethoxy)Phenyl)-1,3,4-Oxadiazol-2-Yl)Benzamide within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F602

b:56.5
occ:1.00
 FAD B:LFV602 0.0 56.5 1.0
CBP B:LFV602 1.1 83.4 1.0
FAC B:LFV602 1.9 67.2 1.0
FAE B:LFV602 1.9 56.1 1.0
CAU B:LFV602 2.2 63.5 1.0
O B:MET235 2.3 45.6 1.0
OBA B:LFV602 2.7 62.6 1.0
C B:MET235 3.2 44.7 1.0
NE1 B:TRP238 3.2 39.2 1.0
CD B:PRO237 3.2 30.1 1.0
CA B:MET235 3.8 52.4 1.0
CG B:PRO237 3.9 30.3 1.0
CD1 B:TRP238 3.9 42.3 1.0
CBF B:LFV602 4.0 64.0 1.0
N B:LEU236 4.1 44.8 1.0
CE2 B:TRP238 4.1 42.7 1.0
CA B:LEU236 4.4 48.3 1.0
O B:PHE234 4.4 54.5 1.0
N B:PRO237 4.5 37.0 1.0
CZ2 B:TRP238 4.5 46.3 1.0
N B:MET235 4.6 48.0 1.0
C B:PHE234 4.8 54.0 1.0
CAT B:LFV602 4.9 66.7 1.0
CAJ B:LFV602 4.9 70.6 1.0

Reference:

L.Friggeri, T.Y.Hargrove, Z.Wawrzak, A.L.Blobaum, G.Rachakonda, C.W.Lindsley, F.Villalta, W.D.Nes, M.Botta, F.P.Guengerich, G.I.Lepesheva. Sterol 14 Alpha-Demethylase Structure-Based Design of Vni (( R)- N-(1-(2,4-Dichlorophenyl)-2-(1 H-Imidazol-1-Yl)Ethyl)-4-(5-Phenyl-1,3,4-Oxadiazol-2-Yl) Benzamide)) Derivatives to Target Fungal Infections: Synthesis, Biological Evaluation, and Crystallographic Analysis. J. Med. Chem. V. 61 5679 2018.
ISSN: ISSN 1520-4804
PubMed: 29894182
DOI: 10.1021/ACS.JMEDCHEM.8B00641
Page generated: Thu Aug 1 18:40:25 2024

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