Atomistry » Fluorine » PDB 6cr2-6d27 » 6cr2
Atomistry »
  Fluorine »
    PDB 6cr2-6d27 »
      6cr2 »

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

Last articles

Zn in 9JPJ
Zn in 9JP7
Zn in 9JPK
Zn in 9JPL
Zn in 9GN6
Zn in 9GN7
Zn in 9GKU
Zn in 9GKW
Zn in 9GKX
Zn in 9GL0
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy