Atomistry » Iron » PDB 6ppu-6q9k » 6q2t
Atomistry »
  Iron »
    PDB 6ppu-6q9k »
      6q2t »

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: Wed Aug 7 06:50:02 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