Fluorine in PDB 5ae2: Ether Lipid-Generating Enzyme Agps in Complex with Inhibitor 1E

The structure of Ether Lipid-Generating Enzyme Agps in Complex with Inhibitor 1E, PDB code: 5ae2 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)	107.06 / 2.00
Space group	P 1
Cell size a, b, c (Å), α, β, γ (°)	60.530, 98.570, 107.070, 90.57, 90.14, 95.67
R / Rfree (%)	17.501 / 22.882

The binding sites of Fluorine atom in the Ether Lipid-Generating Enzyme Agps in Complex with Inhibitor 1E (pdb code 5ae2). 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 1E, PDB code: 5ae2:
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 1E


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 1E within 5.0Å range: probe atom residue distance (Å) B Occ A:F888 b:59.8 occ:1.00 F1 A:FYC888 0.0 59.8 1.0 C16 A:FYC888 1.3 61.2 1.0 C15 A:FYC888 2.3 60.6 1.0 C11 A:FYC888 2.4 61.2 1.0 C10 A:FYC888 2.9 54.4 1.0 C A:GLU526 3.4 24.1 1.0 N A:GLU526 3.4 25.1 1.0 O A:GLU526 3.4 22.1 1.0 CD1 A:TYR580 3.4 33.5 1.0 C14 A:FYC888 3.6 64.1 1.0 C8 A:FYC888 3.6 50.5 1.0 CA A:GLU526 3.6 27.5 1.0 C12 A:FYC888 3.6 63.3 1.0 N A:SER527 3.9 20.5 1.0 C A:GLY525 3.9 25.8 1.0 O A:PHE581 3.9 24.0 1.0 CB A:TYR580 3.9 28.7 1.0 C9 A:FYC888 4.0 54.1 1.0 C13 A:FYC888 4.1 66.0 1.0 CG A:TYR580 4.1 30.3 1.0 N A:PHE581 4.3 23.4 1.0 CE1 A:TYR580 4.4 35.3 1.0 CA A:TYR580 4.4 25.0 1.0 CA A:GLY525 4.4 26.9 1.0 O A:GLY525 4.5 26.4 1.0 CA A:SER527 4.6 22.8 1.0 O2 A:FYC888 4.6 44.6 1.0 C7 A:FYC888 4.6 45.6 1.0 C A:PHE581 4.6 23.4 1.0 C A:TYR580 4.8 25.1 1.0 CB A:SER527 4.8 23.5 1.0

Fluorine binding site 2 out of 4 in the Ether Lipid-Generating Enzyme Agps in Complex with Inhibitor 1E


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 1E within 5.0Å range: probe atom residue distance (Å) B Occ B:F888 b:62.8 occ:1.00 F1 B:FYC888 0.0 62.8 1.0 C16 B:FYC888 1.3 58.8 1.0 C15 B:FYC888 2.3 55.6 1.0 C11 B:FYC888 2.4 55.9 1.0 C10 B:FYC888 2.8 55.1 1.0 C B:GLU526 3.1 27.4 1.0 CD1 B:TYR580 3.1 36.4 1.0 O B:GLU526 3.2 22.0 1.0 N B:GLU526 3.4 32.6 1.0 N B:SER527 3.5 25.0 1.0 CA B:GLU526 3.5 31.3 1.0 C14 B:FYC888 3.6 57.1 1.0 C12 B:FYC888 3.7 57.4 1.0 C8 B:FYC888 3.8 53.4 1.0 CB B:TYR580 3.8 27.8 1.0 CG B:TYR580 3.8 32.9 1.0 C B:GLY525 4.0 30.9 1.0 CE1 B:TYR580 4.0 39.0 1.0 O B:PHE581 4.1 26.5 1.0 C13 B:FYC888 4.1 57.6 1.0 CA B:TYR580 4.2 26.1 1.0 CA B:SER527 4.2 26.6 1.0 O2 B:FYC888 4.3 49.3 1.0 N B:PHE581 4.3 21.8 1.0 CB B:SER527 4.4 25.9 1.0 CA B:GLY525 4.5 32.4 1.0 C9 B:FYC888 4.5 56.4 1.0 C7 B:FYC888 4.5 50.1 1.0 O B:GLY525 4.7 26.5 1.0 C B:TYR580 4.8 24.1 1.0 C B:PHE581 4.9 25.9 1.0

Fluorine binding site 3 out of 4 in the Ether Lipid-Generating Enzyme Agps in Complex with Inhibitor 1E


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 1E within 5.0Å range: probe atom residue distance (Å) B Occ C:F888 b:57.0 occ:1.00 F1 C:FYC888 0.0 57.0 1.0 C16 C:FYC888 1.3 51.2 1.0 C11 C:FYC888 2.3 49.6 1.0 C15 C:FYC888 2.3 52.7 1.0 C10 C:FYC888 2.7 47.3 1.0 CD1 C:TYR580 3.1 34.5 1.0 O C:GLU526 3.1 21.1 1.0 C8 C:FYC888 3.1 42.7 1.0 C C:GLU526 3.2 24.5 1.0 C9 C:FYC888 3.5 44.0 1.0 N C:SER527 3.6 20.9 1.0 C12 C:FYC888 3.6 52.4 1.0 C14 C:FYC888 3.6 50.0 1.0 N C:GLU526 3.6 25.4 1.0 CA C:GLU526 3.7 27.4 1.0 CB C:TYR580 3.8 28.1 1.0 CG C:TYR580 3.9 33.8 1.0 CE1 C:TYR580 4.0 35.2 1.0 C13 C:FYC888 4.1 51.2 1.0 CA C:SER527 4.1 21.7 1.0 C C:GLY525 4.2 27.2 1.0 C7 C:FYC888 4.2 41.1 1.0 CA C:TYR580 4.2 25.4 1.0 O C:PHE581 4.3 26.2 1.0 CB C:SER527 4.3 21.9 1.0 O2 C:FYC888 4.3 45.0 1.0 N C:PHE581 4.5 23.2 1.0 O C:GLY525 4.7 24.3 1.0 CA C:GLY525 4.8 28.1 1.0 C C:TYR580 4.9 24.1 1.0

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


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 1E within 5.0Å range: probe atom residue distance (Å) B Occ D:F888 b:51.9 occ:1.00 F1 D:FYC888 0.0 51.9 1.0 C16 D:FYC888 1.3 55.0 1.0 C15 D:FYC888 2.3 57.5 1.0 C11 D:FYC888 2.4 55.4 1.0 C10 D:FYC888 2.9 51.4 1.0 CD1 D:TYR580 3.2 41.0 1.0 C D:GLU526 3.2 24.6 1.0 O D:GLU526 3.2 25.3 1.0 C8 D:FYC888 3.3 48.1 1.0 N D:GLU526 3.4 25.9 1.0 C9 D:FYC888 3.4 45.9 1.0 C14 D:FYC888 3.6 58.7 1.0 N D:SER527 3.6 24.1 1.0 CA D:GLU526 3.6 26.8 1.0 C12 D:FYC888 3.6 56.6 1.0 CB D:TYR580 3.6 30.7 1.0 CG D:TYR580 3.8 37.0 1.0 C D:GLY525 4.1 27.7 1.0 CA D:TYR580 4.1 28.9 1.0 C13 D:FYC888 4.1 58.6 1.0 CE1 D:TYR580 4.2 39.2 1.0 CA D:SER527 4.2 21.7 1.0 N D:PHE581 4.2 27.1 1.0 O D:PHE581 4.2 25.9 1.0 CB D:SER527 4.3 22.1 1.0 C7 D:FYC888 4.5 47.1 1.0 CA D:GLY525 4.5 27.8 1.0 C D:TYR580 4.7 27.4 1.0 O2 D:FYC888 4.7 49.9 1.0 O D:GLY525 4.7 28.8 1.0 C D:PHE581 4.9 29.5 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