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Chlorine 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:

Fluorine (F) 8 atoms
Iron (Fe) 2 atoms

Chlorine Binding Sites:

The binding sites of Chlorine 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 Chlorine atom.
In total 4 binding sites of Chlorine 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 Chlorine binding site number: 1; 2; 3; 4;

Chlorine binding site 1 out of 4 in 6cr2

Go back to Chlorine Binding Sites List in 6cr2
Chlorine binding site 1 out of 4 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 Chlorine with other atoms in the Cl 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:Cl602

b:44.0
occ:1.00
 CLG A:LFV602 0.0 44.0 1.0
CBG A:LFV602 1.7 33.0 1.0
CBK A:LFV602 2.7 31.3 1.0
CAS A:LFV602 2.7 32.4 1.0
CBN A:LFV602 2.9 34.2 1.0
N A:ALA307 3.3 30.8 1.0
CA A:ALA307 3.4 27.8 1.0
OAA A:LFV602 3.6 65.4 1.0
CZ A:PHE130 3.6 32.2 1.0
C A:MET306 3.7 30.6 1.0
CB A:MET306 3.8 31.9 1.0
NAZ A:LFV602 3.8 43.0 1.0
CB A:ALA307 3.9 30.1 1.0
O A:MET306 3.9 28.5 1.0
CE1 A:PHE130 4.0 28.8 1.0
CAP A:LFV602 4.0 37.4 1.0
CBD A:LFV602 4.0 34.4 1.0
CBC A:LFV602 4.0 53.8 1.0
CAQ A:LFV602 4.1 30.8 1.0
CAV A:LFV602 4.1 29.7 1.0
O A:ALA303 4.2 29.5 1.0
NBO A:LFV602 4.4 27.6 1.0
CA A:MET306 4.4 28.2 1.0
CAI A:LFV602 4.5 41.7 1.0
CZ A:PHE229 4.5 42.1 1.0
C A:ALA307 4.7 24.0 1.0
CE2 A:PHE130 4.7 33.8 1.0
CZ A:PHE504 4.7 65.6 1.0

Chlorine binding site 2 out of 4 in 6cr2

Go back to Chlorine Binding Sites List in 6cr2
Chlorine binding site 2 out of 4 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 Chlorine with other atoms in the Cl 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:Cl602

b:42.5
occ:1.00
 CLF A:LFV602 0.0 42.5 1.0
CBD A:LFV602 1.7 34.4 1.0
CAI A:LFV602 2.7 41.7 1.0
CAS A:LFV602 2.7 32.4 1.0
CMD A:HEM601 3.8 23.9 1.0
CG2 A:VAL135 3.8 33.9 1.0
CB A:ALA303 3.8 29.6 1.0
CAP A:LFV602 4.0 37.4 1.0
CBG A:LFV602 4.0 33.0 1.0
O A:ALA303 4.1 29.5 1.0
C A:ALA303 4.4 28.0 1.0
C2D A:HEM601 4.4 25.0 1.0
CBK A:LFV602 4.5 31.3 1.0
CA A:ALA303 4.7 29.7 1.0
CE2 A:PHE130 4.7 33.8 1.0
CG1 A:VAL135 4.7 37.0 1.0
CB A:ALA307 4.8 30.1 1.0
CD2 A:LEU304 4.9 24.4 1.0
CB A:VAL135 4.9 34.6 1.0

Chlorine binding site 3 out of 4 in 6cr2

Go back to Chlorine Binding Sites List in 6cr2
Chlorine binding site 3 out of 4 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 Chlorine with other atoms in the Cl 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
B:Cl602

b:36.0
occ:1.00
 CLG B:LFV602 0.0 36.0 1.0
CBG B:LFV602 1.8 30.7 1.0
CBK B:LFV602 2.7 31.8 1.0
CAS B:LFV602 2.8 28.9 1.0
CBN B:LFV602 3.0 39.9 1.0
OAA B:LFV602 3.2 51.1 1.0
N B:ALA307 3.5 20.3 1.0
CZ B:PHE130 3.5 22.6 1.0
CA B:ALA307 3.6 20.6 1.0
CB B:MET306 3.6 24.7 1.0
C B:MET306 3.7 23.1 1.0
CE1 B:PHE130 3.8 22.1 1.0
NAZ B:LFV602 3.9 39.9 1.0
CBC B:LFV602 3.9 47.5 1.0
O B:MET306 3.9 22.1 1.0
CAP B:LFV602 4.0 27.9 1.0
CBD B:LFV602 4.0 35.1 1.0
CZ B:PHE229 4.1 28.7 1.0
CB B:ALA307 4.2 20.0 1.0
CAV B:LFV602 4.2 33.2 1.0
CD2 B:HIS310 4.3 48.9 1.0
O B:ALA303 4.3 17.9 1.0
CA B:MET306 4.3 22.1 1.0
NBO B:LFV602 4.5 37.8 1.0
CAQ B:LFV602 4.5 35.2 1.0
CZ B:PHE504 4.5 66.9 1.0
CAI B:LFV602 4.5 37.7 1.0
CE2 B:PHE130 4.7 23.4 1.0
CE2 B:PHE229 4.8 29.9 1.0
CG B:MET306 4.8 29.0 1.0
CE2 B:PHE504 4.9 71.1 1.0
CE1 B:PHE229 4.9 27.4 1.0
C B:ALA307 4.9 22.8 1.0

Chlorine binding site 4 out of 4 in 6cr2

Go back to Chlorine Binding Sites List in 6cr2
Chlorine binding site 4 out of 4 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 Chlorine with other atoms in the Cl 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
B:Cl602

b:38.4
occ:1.00
 CLF B:LFV602 0.0 38.4 1.0
CBD B:LFV602 1.7 35.1 1.0
CAI B:LFV602 2.6 37.7 1.0
CAS B:LFV602 2.8 28.9 1.0
CB B:ALA303 3.7 21.5 1.0
CMD B:HEM601 3.9 16.6 1.0
CG2 B:VAL135 3.9 33.7 1.0
CAP B:LFV602 4.0 27.9 1.0
CG1 B:VAL135 4.0 30.3 1.0
CBG B:LFV602 4.0 30.7 1.0
O B:ALA303 4.2 17.9 1.0
C B:ALA303 4.4 19.4 1.0
C2D B:HEM601 4.5 16.3 1.0
CBK B:LFV602 4.5 31.8 1.0
CA B:ALA303 4.6 20.0 1.0
CB B:VAL135 4.6 32.7 1.0
CE2 B:PHE130 4.6 23.4 1.0
CB B:ALA307 4.8 20.0 1.0
CZ B:PHE130 4.9 22.6 1.0
N B:LEU304 5.0 19.3 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: Fri Jul 26 23:40:55 2024

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