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Iron 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
Chlorine (Cl) 4 atoms

Iron Binding Sites:

The binding sites of Iron 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 Iron atom.
In total 2 binding sites of Iron 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 Iron binding site number: 1; 2;

Iron binding site 1 out of 2 in 6cr2

Go back to Iron Binding Sites List in 6cr2
Iron binding site 1 out of 2 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 Iron with other atoms in the Fe 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:Fe601

b:23.0
occ:1.00
 FE A:HEM601 0.0 23.0 1.0
ND A:HEM601 1.8 25.6 1.0
NA A:HEM601 2.0 21.6 1.0
NAW A:LFV602 2.0 30.1 1.0
NC A:HEM601 2.1 22.2 1.0
NB A:HEM601 2.1 22.2 1.0
SG A:CYS463 2.3 22.6 1.0
C4D A:HEM601 2.8 20.0 1.0
C1D A:HEM601 2.9 24.5 1.0
CAR A:LFV602 2.9 27.9 1.0
C1A A:HEM601 3.0 22.3 1.0
CAH A:LFV602 3.0 23.7 1.0
C4A A:HEM601 3.1 23.1 1.0
C4C A:HEM601 3.1 25.1 1.0
C4B A:HEM601 3.1 19.9 1.0
C1B A:HEM601 3.1 23.2 1.0
C1C A:HEM601 3.2 23.4 1.0
CB A:CYS463 3.3 23.3 1.0
CHA A:HEM601 3.3 20.3 1.0
CHD A:HEM601 3.4 24.4 1.0
CHB A:HEM601 3.5 21.6 1.0
CHC A:HEM601 3.5 20.3 1.0
CA A:CYS463 4.0 25.7 1.0
NBO A:LFV602 4.1 27.6 1.0
CAQ A:LFV602 4.1 30.8 1.0
C3D A:HEM601 4.1 24.7 1.0
C2D A:HEM601 4.1 25.0 1.0
C2A A:HEM601 4.2 23.4 1.0
C3A A:HEM601 4.2 22.8 1.0
C3C A:HEM601 4.3 23.7 1.0
C2B A:HEM601 4.3 22.8 1.0
C2C A:HEM601 4.3 21.4 1.0
C3B A:HEM601 4.3 21.5 1.0
N A:GLY465 4.9 24.3 1.0

Iron binding site 2 out of 2 in 6cr2

Go back to Iron Binding Sites List in 6cr2
Iron binding site 2 out of 2 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 Iron with other atoms in the Fe 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
B:Fe601

b:19.6
occ:1.00
 FE B:HEM601 0.0 19.6 1.0
ND B:HEM601 1.9 16.8 1.0
NA B:HEM601 2.0 16.7 1.0
NAW B:LFV602 2.0 29.4 1.0
NC B:HEM601 2.1 16.7 1.0
NB B:HEM601 2.1 16.9 1.0
SG B:CYS463 2.4 21.2 1.0
C4D B:HEM601 2.8 14.3 1.0
C1D B:HEM601 2.9 16.4 1.0
C1A B:HEM601 2.9 17.0 1.0
CAH B:LFV602 3.0 29.7 1.0
CAR B:LFV602 3.0 35.9 1.0
C4B B:HEM601 3.1 16.4 1.0
C4A B:HEM601 3.1 18.2 1.0
C4C B:HEM601 3.1 16.6 1.0
C1B B:HEM601 3.1 17.8 1.0
C1C B:HEM601 3.1 17.4 1.0
CHA B:HEM601 3.3 14.8 1.0
CHD B:HEM601 3.4 17.0 1.0
CB B:CYS463 3.4 22.0 1.0
CHB B:HEM601 3.5 19.2 1.0
CHC B:HEM601 3.5 16.1 1.0
C3D B:HEM601 4.1 17.8 1.0
CAQ B:LFV602 4.1 35.2 1.0
C2D B:HEM601 4.1 16.3 1.0
NBO B:LFV602 4.2 37.8 1.0
C2A B:HEM601 4.2 18.7 1.0
CA B:CYS463 4.2 21.1 1.0
C3A B:HEM601 4.2 16.3 1.0
C3C B:HEM601 4.3 16.1 1.0
C2B B:HEM601 4.3 18.3 1.0
C2C B:HEM601 4.3 16.9 1.0
C3B B:HEM601 4.3 18.9 1.0
N B:GLY465 5.0 22.5 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: Tue Aug 6 15:11:48 2024

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