Fluorine in PDB 5ae1: Ether Lipid-Generating Enzyme Agps in Complex with Inhibitor ZINC69435460

All present enzymatic activity of Ether Lipid-Generating Enzyme Agps in Complex with Inhibitor ZINC69435460:
2.5.1.26;

The structure of Ether Lipid-Generating Enzyme Agps in Complex with Inhibitor ZINC69435460, PDB code: 5ae1 was solved by V.Piano, D.I.Benjamin, S.Valente, S.Nenci, B.Marrocco, A.Mai, A.Aliverti, D.K.Nomura, A.Mattevi, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	107.01 / 2.10
Space group	P 1
Cell size a, b, c (Å), α, β, γ (°)	60.790, 99.020, 107.020, 90.64, 89.96, 95.49
R / Rfree (%)	18.628 / 22.921

The binding sites of Fluorine atom in the Ether Lipid-Generating Enzyme Agps in Complex with Inhibitor ZINC69435460 (pdb code 5ae1). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 4 binding sites of Fluorine where determined in the Ether Lipid-Generating Enzyme Agps in Complex with Inhibitor ZINC69435460, PDB code: 5ae1:
Jump to Fluorine binding site number: 1; 2; 3; 4;

Fluorine binding site 1 out of 4 in the Ether Lipid-Generating Enzyme Agps in Complex with Inhibitor ZINC69435460


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of Ether Lipid-Generating Enzyme Agps in Complex with Inhibitor ZINC69435460 within 5.0Å range: probe atom residue distance (Å) B Occ A:F888 b:65.0 occ:1.00 F A:B2Z888 0.0 65.0 1.0 C18 A:B2Z888 1.4 56.5 1.0 C13 A:B2Z888 2.4 53.0 1.0 C17 A:B2Z888 2.4 55.9 1.0 C1 A:B2Z888 2.7 46.3 1.0 N A:GLU526 2.9 32.9 1.0 C A:GLU526 3.1 29.1 1.0 CA A:GLU526 3.1 33.8 1.0 C A:GLY525 3.2 35.0 1.0 O A:GLU526 3.3 27.8 1.0 C2 A:B2Z888 3.5 41.4 1.0 O A:PHE581 3.5 28.4 1.0 N A:SER527 3.6 28.1 1.0 C14 A:B2Z888 3.7 55.8 1.0 C16 A:B2Z888 3.7 57.5 1.0 O A:GLY525 3.7 32.8 1.0 CA A:GLY525 3.8 38.9 1.0 C A:B2Z888 4.0 47.7 1.0 CD1 A:TYR580 4.1 35.9 1.0 C15 A:B2Z888 4.1 58.5 1.0 O A:B2Z888 4.2 34.6 1.0 N A:PHE581 4.3 32.8 1.0 CB A:TYR580 4.3 32.3 1.0 C3 A:B2Z888 4.4 37.0 1.0 C A:PHE581 4.4 33.2 1.0 CA A:SER527 4.5 27.4 1.0 CA A:TYR580 4.6 30.0 1.0 CB A:GLU526 4.7 37.0 1.0 CG A:TYR580 4.7 34.0 1.0 N A:GLY525 4.8 39.2 1.0 CB A:ALA582 4.9 30.8 1.0 C A:TYR580 4.9 33.1 1.0 CB A:SER527 4.9 28.4 1.0

Fluorine binding site 2 out of 4 in the Ether Lipid-Generating Enzyme Agps in Complex with Inhibitor ZINC69435460


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of Ether Lipid-Generating Enzyme Agps in Complex with Inhibitor ZINC69435460 within 5.0Å range: probe atom residue distance (Å) B Occ B:F888 b:70.4 occ:1.00 F B:B2Z888 0.0 70.4 1.0 C18 B:B2Z888 1.4 58.5 1.0 C17 B:B2Z888 2.4 57.0 1.0 C13 B:B2Z888 2.4 52.5 1.0 C1 B:B2Z888 2.8 48.7 1.0 N B:GLU526 3.0 34.5 1.0 C B:GLU526 3.2 31.9 1.0 CA B:GLU526 3.3 35.7 1.0 C B:GLY525 3.3 31.3 1.0 O B:GLU526 3.3 30.9 1.0 C2 B:B2Z888 3.6 44.0 1.0 O B:PHE581 3.6 30.2 1.0 C16 B:B2Z888 3.6 56.2 1.0 C14 B:B2Z888 3.7 56.6 1.0 N B:SER527 3.7 28.2 1.0 O B:GLY525 3.8 25.9 1.0 CA B:GLY525 3.9 34.6 1.0 CD1 B:TYR580 4.1 39.0 1.0 C B:B2Z888 4.1 49.0 1.0 C15 B:B2Z888 4.1 58.9 1.0 O B:B2Z888 4.2 38.2 1.0 CB B:TYR580 4.3 33.9 1.0 C3 B:B2Z888 4.4 41.6 1.0 N B:PHE581 4.4 27.2 1.0 C B:PHE581 4.5 30.5 1.0 CA B:SER527 4.6 27.2 1.0 CB B:ALA582 4.7 23.8 1.0 CG B:TYR580 4.7 35.3 1.0 CA B:TYR580 4.7 28.4 1.0 CB B:GLU526 4.8 37.7 1.0 N B:GLY525 4.9 31.9 1.0

Fluorine binding site 3 out of 4 in the Ether Lipid-Generating Enzyme Agps in Complex with Inhibitor ZINC69435460


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of Ether Lipid-Generating Enzyme Agps in Complex with Inhibitor ZINC69435460 within 5.0Å range: probe atom residue distance (Å) B Occ C:F888 b:53.9 occ:1.00 F C:B2Z888 0.0 53.9 1.0 C18 C:B2Z888 1.3 41.2 1.0 C13 C:B2Z888 2.3 34.7 1.0 C17 C:B2Z888 2.3 39.7 1.0 C1 C:B2Z888 2.8 34.5 1.0 N C:GLU526 3.0 27.7 1.0 C C:GLU526 3.1 28.8 1.0 CA C:GLU526 3.3 28.3 1.0 O C:GLU526 3.3 29.1 1.0 O C:PHE581 3.4 28.2 1.0 C C:GLY525 3.5 30.9 1.0 N C:SER527 3.6 23.5 1.0 C14 C:B2Z888 3.6 37.6 1.0 C2 C:B2Z888 3.6 32.2 1.0 C16 C:B2Z888 3.6 37.8 1.0 CD1 C:TYR580 3.9 33.5 1.0 C C:B2Z888 4.0 34.7 1.0 O C:GLY525 4.0 31.1 1.0 C15 C:B2Z888 4.1 36.7 1.0 CA C:GLY525 4.1 31.7 1.0 CB C:TYR580 4.1 27.8 1.0 N C:PHE581 4.2 24.9 1.0 O C:B2Z888 4.3 30.2 1.0 CA C:SER527 4.4 23.8 1.0 C C:PHE581 4.5 28.3 1.0 C3 C:B2Z888 4.5 33.1 1.0 CG C:TYR580 4.5 31.9 1.0 CA C:TYR580 4.5 27.3 1.0 CB C:GLU526 4.8 30.4 1.0 CB C:SER527 4.8 23.9 1.0 CE1 C:TYR580 4.9 35.8 1.0 C C:TYR580 4.9 26.5 1.0 CB C:ALA582 5.0 26.4 1.0

Fluorine binding site 4 out of 4 in the Ether Lipid-Generating Enzyme Agps in Complex with Inhibitor ZINC69435460


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 4 of Ether Lipid-Generating Enzyme Agps in Complex with Inhibitor ZINC69435460 within 5.0Å range: probe atom residue distance (Å) B Occ D:F888 b:56.4 occ:1.00 F D:B2Z888 0.0 56.4 1.0 C18 D:B2Z888 1.3 50.2 1.0 C17 D:B2Z888 2.4 51.8 1.0 C13 D:B2Z888 2.4 50.8 1.0 C1 D:B2Z888 2.9 48.0 1.0 C D:GLU526 3.1 31.6 1.0 O D:GLU526 3.3 31.0 1.0 CD1 D:TYR580 3.3 42.0 1.0 N D:GLU526 3.4 34.5 1.0 N D:SER527 3.4 28.7 1.0 CA D:GLU526 3.5 32.7 1.0 C16 D:B2Z888 3.7 50.0 1.0 C2 D:B2Z888 3.7 44.2 1.0 C14 D:B2Z888 3.7 51.2 1.0 O D:PHE581 3.7 30.9 1.0 CB D:TYR580 3.7 33.7 1.0 C D:GLY525 3.9 34.5 1.0 CG D:TYR580 4.0 39.8 1.0 CA D:TYR580 4.1 32.6 1.0 CA D:SER527 4.1 29.0 1.0 N D:PHE581 4.1 31.2 1.0 C D:B2Z888 4.2 48.8 1.0 O D:B2Z888 4.2 39.5 1.0 C15 D:B2Z888 4.2 50.7 1.0 CE1 D:TYR580 4.3 45.4 1.0 O D:GLY525 4.4 31.2 1.0 C3 D:B2Z888 4.4 40.1 1.0 CB D:SER527 4.4 28.2 1.0 C D:PHE581 4.5 35.3 1.0 CA D:GLY525 4.5 40.8 1.0 C D:TYR580 4.6 31.8 1.0 CA D:PHE581 5.0 37.0 1.0

V.Piano, D.I.Benjamin, S.Valente, S.Nenci, B.Marrocco, A.Mai, A.Aliverti, D.K.Nomura, A.Mattevi. Discovery of Inhibitors For the Ether Lipid-Generating Enzyme Agps As Anti-Cancer Agents. Acs Chem.Biol. V. 10 2589 2015.
ISSN: ISSN 1554-8929
PubMed: 26322624
DOI: 10.1021/ACSCHEMBIO.5B00466