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Chlorine 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
Iron (Fe) 2 atoms

Chlorine Binding Sites:

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

Chlorine binding site 1 out of 3 in 6q2t

Go back to Chlorine Binding Sites List in 6q2t
Chlorine binding site 1 out of 3 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 Chlorine with other atoms in the Cl 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:Cl602

b:91.1
occ:1.00
 CLA A:PJM602 0.0 91.1 1.0
CBK A:PJM602 1.7 88.6 1.0
CAW A:PJM602 2.7 77.3 1.0
CBR A:PJM602 2.7 92.1 1.0
CBV A:PJM602 2.9 94.9 1.0
N A:ALA311 3.2 78.9 1.0
CA A:ALA311 3.4 83.7 1.0
C A:LEU310 3.5 77.9 1.0
CAR A:PJM602 3.6 96.3 1.0
CB A:LEU310 3.6 87.1 1.0
O A:LEU310 3.8 78.1 1.0
NBW A:PJM602 3.9 93.0 1.0
CBO A:PJM602 4.0 84.3 1.0
NBE A:PJM602 4.0 95.0 1.0
CAY A:PJM602 4.0 90.8 1.0
CAQ A:PJM602 4.0 83.8 1.0
CB A:ALA311 4.1 75.0 1.0
CZ A:PHE139 4.1 99.5 1.0
CA A:LEU310 4.2 86.3 1.0
CE1 A:PHE139 4.3 0.2 1.0
OAA A:PJM602 4.4 0.7 1.0
O A:GLY307 4.4 80.6 1.0
CAF A:PJM602 4.5 0.8 1.0
CAP A:PJM602 4.5 82.2 1.0
CBG A:PJM602 4.6 0.1 1.0
C A:ALA311 4.7 90.6 1.0
CE2 A:PHE234 4.8 71.8 1.0
CAT A:PJM602 4.9 98.1 1.0
CG A:LEU310 5.0 80.5 1.0
CZ A:PHE234 5.0 75.6 1.0

Chlorine binding site 2 out of 3 in 6q2t

Go back to Chlorine Binding Sites List in 6q2t
Chlorine binding site 2 out of 3 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 Chlorine with other atoms in the Cl 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
A:Cl611

b:1.0
occ:1.00
 CLA A:PJM611 0.0 1.0 1.0
CBK A:PJM611 1.7 0.0 1.0
CAW A:PJM611 2.7 0.6 1.0
CBR A:PJM611 2.7 0.7 1.0
CAY A:PJM611 2.9 0.5 1.0
CBV A:PJM611 3.0 0.3 1.0
NBW A:PJM611 3.7 0.6 1.0
CAQ A:PJM611 4.0 0.2 1.0
CBO A:PJM611 4.0 0.1 1.0
CAT A:PJM611 4.0 0.7 1.0
O A:GLY102 4.1 80.8 1.0
O A:VAL101 4.2 71.8 1.0
C A:GLY102 4.4 73.2 1.0
NBE A:PJM611 4.5 0.1 1.0
CE1 A:PHE70 4.5 54.2 1.0
CAP A:PJM611 4.5 1.0 1.0
CA A:GLY102 4.5 76.0 1.0
NZ A:LYS103 4.6 0.3 1.0
CD A:LYS103 4.7 0.0 1.0
CAR A:PJM611 4.7 0.5 1.0
CZ A:PHE70 4.7 52.2 1.0
CE A:LYS103 4.9 0.4 1.0

Chlorine binding site 3 out of 3 in 6q2t

Go back to Chlorine Binding Sites List in 6q2t
Chlorine binding site 3 out of 3 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 Chlorine with other atoms in the Cl binding site number 3 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:Cl602

b:87.5
occ:1.00
 CLA B:PJM602 0.0 87.5 1.0
CBK B:PJM602 1.7 87.2 1.0
CAW B:PJM602 2.7 90.0 1.0
CBR B:PJM602 2.7 80.6 1.0
CBV B:PJM602 3.0 83.4 1.0
N B:ALA311 3.2 76.4 1.0
C B:LEU310 3.3 78.0 1.0
CA B:ALA311 3.3 95.4 1.0
O B:LEU310 3.5 75.2 1.0
CAR B:PJM602 3.5 77.3 1.0
CB B:LEU310 3.7 87.0 1.0
NBW B:PJM602 3.9 74.5 1.0
CBO B:PJM602 4.0 83.0 1.0
CAQ B:PJM602 4.0 76.4 1.0
NBE B:PJM602 4.0 95.4 1.0
CAY B:PJM602 4.0 79.5 1.0
CA B:LEU310 4.1 84.7 1.0
CB B:ALA311 4.1 98.4 1.0
CZ B:PHE139 4.4 58.0 1.0
CAF B:PJM602 4.4 70.0 1.0
O B:GLY307 4.4 58.1 1.0
CAP B:PJM602 4.5 74.6 1.0
C B:ALA311 4.5 0.6 1.0
OAA B:PJM602 4.6 0.5 1.0
CE1 B:PHE139 4.7 65.2 1.0
CBG B:PJM602 4.7 0.6 1.0
CE2 B:PHE234 4.7 64.6 1.0
O B:ALA311 4.8 0.0 1.0
CAT B:PJM602 4.9 75.0 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: Mon Jul 29 13:43:26 2024

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