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Iron in PDB 6q2t: Human Sterol 14A-Demethylase (CYP51) in Complex with the Functionally Irreversible Inhibitor (R)-N-(1-(3-Chloro-4'-Fluoro-[1,1'-Biphenyl]- 4-Yl)-2-(1H-Imidazol-1-Yl)Ethyl)-4-(5-(3-Fluoro-5-(5-Fluoropyrimidin- 4-Yl)Phenyl)-1,3,4-Oxadiazol-2-Yl)Benzamide

Enzymatic activity of Human Sterol 14A-Demethylase (CYP51) in Complex with the Functionally Irreversible Inhibitor (R)-N-(1-(3-Chloro-4'-Fluoro-[1,1'-Biphenyl]- 4-Yl)-2-(1H-Imidazol-1-Yl)Ethyl)-4-(5-(3-Fluoro-5-(5-Fluoropyrimidin- 4-Yl)Phenyl)-1,3,4-Oxadiazol-2-Yl)Benzamide

All present enzymatic activity of Human Sterol 14A-Demethylase (CYP51) in Complex with the Functionally Irreversible Inhibitor (R)-N-(1-(3-Chloro-4'-Fluoro-[1,1'-Biphenyl]- 4-Yl)-2-(1H-Imidazol-1-Yl)Ethyl)-4-(5-(3-Fluoro-5-(5-Fluoropyrimidin- 4-Yl)Phenyl)-1,3,4-Oxadiazol-2-Yl)Benzamide:
1.14.13.70; 1.14.14.154;

Protein crystallography data

The structure of Human Sterol 14A-Demethylase (CYP51) in Complex with the Functionally Irreversible Inhibitor (R)-N-(1-(3-Chloro-4'-Fluoro-[1,1'-Biphenyl]- 4-Yl)-2-(1H-Imidazol-1-Yl)Ethyl)-4-(5-(3-Fluoro-5-(5-Fluoropyrimidin- 4-Yl)Phenyl)-1,3,4-Oxadiazol-2-Yl)Benzamide, PDB code: 6q2t 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) 28.10 / 2.80
Space group I 4
Cell size a, b, c (Å), α, β, γ (°) 117.664, 117.664, 157.842, 90.00, 90.00, 90.00
R / Rfree (%) 22.7 / 25.6

Other elements in 6q2t:

The structure of Human Sterol 14A-Demethylase (CYP51) in Complex with the Functionally Irreversible Inhibitor (R)-N-(1-(3-Chloro-4'-Fluoro-[1,1'-Biphenyl]- 4-Yl)-2-(1H-Imidazol-1-Yl)Ethyl)-4-(5-(3-Fluoro-5-(5-Fluoropyrimidin- 4-Yl)Phenyl)-1,3,4-Oxadiazol-2-Yl)Benzamide also contains other interesting chemical elements:

Fluorine (F) 9 atoms
Chlorine (Cl) 3 atoms

Iron Binding Sites:

The binding sites of Iron atom in the Human Sterol 14A-Demethylase (CYP51) in Complex with the Functionally Irreversible Inhibitor (R)-N-(1-(3-Chloro-4'-Fluoro-[1,1'-Biphenyl]- 4-Yl)-2-(1H-Imidazol-1-Yl)Ethyl)-4-(5-(3-Fluoro-5-(5-Fluoropyrimidin- 4-Yl)Phenyl)-1,3,4-Oxadiazol-2-Yl)Benzamide (pdb code 6q2t). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 2 binding sites of Iron where determined in the Human Sterol 14A-Demethylase (CYP51) in Complex with the Functionally Irreversible Inhibitor (R)-N-(1-(3-Chloro-4'-Fluoro-[1,1'-Biphenyl]- 4-Yl)-2-(1H-Imidazol-1-Yl)Ethyl)-4-(5-(3-Fluoro-5-(5-Fluoropyrimidin- 4-Yl)Phenyl)-1,3,4-Oxadiazol-2-Yl)Benzamide, PDB code: 6q2t:
Jump to Iron binding site number: 1; 2;

Iron binding site 1 out of 2 in 6q2t

Go back to Iron Binding Sites List in 6q2t
Iron binding site 1 out of 2 in the Human Sterol 14A-Demethylase (CYP51) in Complex with the Functionally Irreversible Inhibitor (R)-N-(1-(3-Chloro-4'-Fluoro-[1,1'-Biphenyl]- 4-Yl)-2-(1H-Imidazol-1-Yl)Ethyl)-4-(5-(3-Fluoro-5-(5-Fluoropyrimidin- 4-Yl)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 Human Sterol 14A-Demethylase (CYP51) in Complex with the Functionally Irreversible Inhibitor (R)-N-(1-(3-Chloro-4'-Fluoro-[1,1'-Biphenyl]- 4-Yl)-2-(1H-Imidazol-1-Yl)Ethyl)-4-(5-(3-Fluoro-5-(5-Fluoropyrimidin- 4-Yl)Phenyl)-1,3,4-Oxadiazol-2-Yl)Benzamide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe601

b:82.5
occ:1.00
 FE A:HEM601 0.0 82.5 1.0
ND A:HEM601 1.9 74.0 1.0
NA A:HEM601 2.0 69.1 1.0
NC A:HEM601 2.1 76.8 1.0
NAZ A:PJM602 2.1 0.5 1.0
NB A:HEM601 2.1 66.3 1.0
SG A:CYS449 2.2 91.2 1.0
C4D A:HEM601 2.9 73.8 1.0
C1D A:HEM601 2.9 74.7 1.0
C1A A:HEM601 3.0 67.0 1.0
CAT A:PJM602 3.0 98.1 1.0
C4C A:HEM601 3.1 83.1 1.0
C4A A:HEM601 3.1 65.5 1.0
C1B A:HEM601 3.1 63.3 1.0
C4B A:HEM601 3.1 69.3 1.0
CAF A:PJM602 3.1 0.8 1.0
C1C A:HEM601 3.2 77.6 1.0
CHA A:HEM601 3.3 71.3 1.0
CHD A:HEM601 3.4 82.6 1.0
CB A:CYS449 3.4 87.0 1.0
CHB A:HEM601 3.5 62.8 1.0
CHC A:HEM601 3.5 73.1 1.0
CA A:CYS449 4.1 86.8 1.0
C3D A:HEM601 4.1 80.2 1.0
C2D A:HEM601 4.1 79.5 1.0
NBW A:PJM602 4.1 93.0 1.0
C2A A:HEM601 4.2 69.6 1.0
CAR A:PJM602 4.2 96.3 1.0
C3A A:HEM601 4.2 69.9 1.0
C3C A:HEM601 4.3 85.3 1.0
C2B A:HEM601 4.3 63.0 1.0
C2C A:HEM601 4.3 79.7 1.0
C3B A:HEM601 4.4 70.7 1.0
N A:ILE450 4.9 98.4 1.0
C A:CYS449 5.0 94.1 1.0

Iron binding site 2 out of 2 in 6q2t

Go back to Iron Binding Sites List in 6q2t
Iron binding site 2 out of 2 in the Human Sterol 14A-Demethylase (CYP51) in Complex with the Functionally Irreversible Inhibitor (R)-N-(1-(3-Chloro-4'-Fluoro-[1,1'-Biphenyl]- 4-Yl)-2-(1H-Imidazol-1-Yl)Ethyl)-4-(5-(3-Fluoro-5-(5-Fluoropyrimidin- 4-Yl)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 Human Sterol 14A-Demethylase (CYP51) in Complex with the Functionally Irreversible Inhibitor (R)-N-(1-(3-Chloro-4'-Fluoro-[1,1'-Biphenyl]- 4-Yl)-2-(1H-Imidazol-1-Yl)Ethyl)-4-(5-(3-Fluoro-5-(5-Fluoropyrimidin- 4-Yl)Phenyl)-1,3,4-Oxadiazol-2-Yl)Benzamide within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe601

b:78.6
occ:1.00
 FE B:HEM601 0.0 78.6 1.0
ND B:HEM601 1.9 79.0 1.0
NA B:HEM601 2.0 71.3 1.0
NAZ B:PJM602 2.1 74.1 1.0
NC B:HEM601 2.1 75.2 1.0
NB B:HEM601 2.1 75.2 1.0
SG B:CYS449 2.4 82.4 1.0
C4D B:HEM601 2.9 79.7 1.0
C1D B:HEM601 2.9 74.2 1.0
C1A B:HEM601 3.0 74.9 1.0
CAT B:PJM602 3.0 75.0 1.0
C4A B:HEM601 3.1 81.6 1.0
C4C B:HEM601 3.1 76.0 1.0
C1B B:HEM601 3.1 72.9 1.0
C4B B:HEM601 3.1 74.4 1.0
CAF B:PJM602 3.1 70.0 1.0
C1C B:HEM601 3.1 76.5 1.0
CB B:CYS449 3.3 73.1 1.0
CHA B:HEM601 3.3 74.2 1.0
CHD B:HEM601 3.4 76.6 1.0
CHB B:HEM601 3.5 74.1 1.0
CHC B:HEM601 3.5 73.3 1.0
CA B:CYS449 4.0 73.3 1.0
NBW B:PJM602 4.1 74.5 1.0
C3D B:HEM601 4.1 80.2 1.0
C2D B:HEM601 4.1 74.6 1.0
CAR B:PJM602 4.2 77.3 1.0
C2A B:HEM601 4.2 77.5 1.0
C3A B:HEM601 4.2 86.5 1.0
C3C B:HEM601 4.3 77.7 1.0
C2B B:HEM601 4.3 72.2 1.0
C2C B:HEM601 4.3 81.0 1.0
C3B B:HEM601 4.3 75.8 1.0
N B:ILE450 4.8 88.9 1.0
C B:CYS449 4.9 79.2 1.0
N B:GLY451 5.0 93.8 1.0

Reference:

L.Friggeri, T.Y.Hargrove, Z.Wawrzak, F.P.Guengerich, G.I.Lepesheva. Validation of Human Sterol 14 Alpha-Demethylase (CYP51) Druggability: Structure-Guided Design, Synthesis and Evaluation of Stoichiometric, Functionally Irreversible Inhibitors. J.Med.Chem. 2019.
ISSN: ISSN 0022-2623
PubMed: 31663733
DOI: 10.1021/ACS.JMEDCHEM.9B01485
Page generated: Sun Dec 13 16:50:11 2020

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