Fluorine in PDB 5adz: Ether Lipid-Generating Enzyme Agps in Complex with Inhibitor 1A

All present enzymatic activity of Ether Lipid-Generating Enzyme Agps in Complex with Inhibitor 1A:
2.5.1.26;

The structure of Ether Lipid-Generating Enzyme Agps in Complex with Inhibitor 1A, PDB code: 5adz 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)	107.96 / 2.20
Space group	P 1
Cell size a, b, c (Å), α, β, γ (°)	61.060, 99.610, 107.970, 90.57, 90.04, 94.76
R / Rfree (%)	19.514 / 25.344

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


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 1A within 5.0Å range: probe atom residue distance (Å) B Occ A:F888 b:38.7 occ:1.00 F A:KQS888 0.0 38.7 1.0 C16 A:KQS888 1.4 39.4 1.0 C15 A:KQS888 2.4 37.6 1.0 C11 A:KQS888 2.4 36.6 1.0 C10 A:KQS888 2.9 31.5 1.0 C A:GLU526 2.9 27.6 1.0 N A:GLU526 2.9 30.6 1.0 O A:GLU526 3.1 24.2 1.0 CA A:GLU526 3.2 32.5 1.0 N A:SER527 3.3 27.1 1.0 O A:PHE581 3.5 28.8 1.0 CD1 A:TYR580 3.6 33.6 1.0 C14 A:KQS888 3.7 39.1 1.0 C12 A:KQS888 3.7 37.2 1.0 C9 A:KQS888 3.7 30.3 1.0 C A:GLY525 3.8 32.3 1.0 N A:PHE581 4.0 26.8 1.0 C17 A:KQS888 4.1 32.1 1.0 CA A:SER527 4.1 28.7 1.0 CB A:TYR580 4.1 30.7 1.0 C13 A:KQS888 4.1 41.4 1.0 CA A:TYR580 4.3 29.4 1.0 CG A:TYR580 4.3 32.6 1.0 CA A:GLY525 4.3 33.0 1.0 O1 A:KQS888 4.4 25.4 1.0 C A:PHE581 4.4 31.1 1.0 O A:GLY525 4.5 30.4 1.0 CB A:SER527 4.5 28.9 1.0 C8 A:KQS888 4.5 27.1 1.0 CE1 A:TYR580 4.6 36.4 1.0 C A:TYR580 4.7 25.5 1.0 CB A:GLU526 4.7 37.5 1.0 CA A:PHE581 4.9 31.6 1.0

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


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 1A within 5.0Å range: probe atom residue distance (Å) B Occ B:F888 b:36.6 occ:1.00 F B:KQS888 0.0 36.6 1.0 C16 B:KQS888 1.4 39.7 1.0 C15 B:KQS888 2.4 40.1 1.0 C11 B:KQS888 2.5 38.6 1.0 C B:GLU526 3.0 35.7 1.0 C10 B:KQS888 3.0 35.0 1.0 O B:GLU526 3.0 31.7 1.0 N B:GLU526 3.1 34.9 1.0 CA B:GLU526 3.3 38.1 1.0 N B:SER527 3.4 31.4 1.0 O B:PHE581 3.6 38.1 1.0 C14 B:KQS888 3.7 38.5 1.0 C B:GLY525 3.7 32.8 1.0 C12 B:KQS888 3.7 37.8 1.0 CD1 B:TYR580 3.8 40.0 1.0 C9 B:KQS888 4.0 35.7 1.0 C17 B:KQS888 4.1 33.8 1.0 C13 B:KQS888 4.2 41.8 1.0 CA B:GLY525 4.2 34.6 1.0 CA B:SER527 4.2 33.1 1.0 N B:PHE581 4.2 36.2 1.0 CB B:TYR580 4.3 37.7 1.0 O B:GLY525 4.3 28.8 1.0 CA B:TYR580 4.4 36.0 1.0 CG B:TYR580 4.5 38.1 1.0 C B:PHE581 4.5 39.4 1.0 O1 B:KQS888 4.5 35.8 1.0 CB B:SER527 4.6 32.5 1.0 CE1 B:TYR580 4.7 43.6 1.0 C8 B:KQS888 4.8 34.8 1.0 CB B:GLU526 4.8 39.4 1.0 C B:TYR580 4.8 35.1 1.0 CB B:ALA582 5.0 35.5 1.0

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


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 1A within 5.0Å range: probe atom residue distance (Å) B Occ C:F888 b:38.3 occ:1.00 F C:KQS888 0.0 38.3 1.0 C16 C:KQS888 1.3 33.7 1.0 C15 C:KQS888 2.4 34.8 1.0 C11 C:KQS888 2.4 32.5 1.0 C C:GLU526 2.8 27.4 1.0 C10 C:KQS888 2.9 29.9 1.0 N C:GLU526 3.1 30.2 1.0 O C:GLU526 3.1 26.4 1.0 CA C:GLU526 3.1 30.0 1.0 N C:SER527 3.1 24.8 1.0 C C:GLY525 3.5 33.5 1.0 C9 C:KQS888 3.5 27.4 1.0 C14 C:KQS888 3.6 33.5 1.0 CD1 C:TYR580 3.7 27.8 1.0 O C:PHE581 3.7 29.2 1.0 C12 C:KQS888 3.7 32.8 1.0 O C:GLY525 3.9 32.1 1.0 CA C:SER527 4.1 24.0 1.0 C13 C:KQS888 4.1 31.4 1.0 O1 C:KQS888 4.1 23.9 1.0 CB C:TYR580 4.2 25.1 1.0 C17 C:KQS888 4.2 31.6 1.0 N C:PHE581 4.2 27.7 1.0 CA C:GLY525 4.3 34.3 1.0 C8 C:KQS888 4.3 26.1 1.0 CG C:TYR580 4.4 27.7 1.0 CA C:TYR580 4.5 25.6 1.0 C C:PHE581 4.6 29.3 1.0 CE1 C:TYR580 4.6 28.8 1.0 CB C:SER527 4.6 23.3 1.0 CB C:GLU526 4.7 31.9 1.0 C C:TYR580 4.9 27.2 1.0

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


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 1A within 5.0Å range: probe atom residue distance (Å) B Occ D:F888 b:54.5 occ:1.00 F D:KQS888 0.0 54.5 1.0 C16 D:KQS888 1.3 49.1 1.0 C15 D:KQS888 2.3 48.2 1.0 C11 D:KQS888 2.5 47.4 1.0 N D:GLU526 3.0 33.7 1.0 C10 D:KQS888 3.0 41.4 1.0 C D:GLU526 3.1 32.0 1.0 CA D:GLU526 3.2 34.5 1.0 O D:GLU526 3.3 29.1 1.0 N D:SER527 3.5 28.2 1.0 C D:GLY525 3.5 34.8 1.0 O D:PHE581 3.5 30.5 1.0 C14 D:KQS888 3.6 46.7 1.0 C12 D:KQS888 3.7 48.9 1.0 CD1 D:TYR580 3.8 35.1 1.0 O D:GLY525 4.0 37.7 1.0 CB D:TYR580 4.0 31.1 1.0 C9 D:KQS888 4.0 39.5 1.0 C17 D:KQS888 4.1 38.9 1.0 C13 D:KQS888 4.1 45.3 1.0 CA D:GLY525 4.2 35.9 1.0 N D:PHE581 4.2 32.7 1.0 CA D:SER527 4.3 30.2 1.0 CA D:TYR580 4.4 31.6 1.0 CG D:TYR580 4.4 34.0 1.0 C D:PHE581 4.4 34.3 1.0 O1 D:KQS888 4.5 39.6 1.0 CB D:SER527 4.7 28.4 1.0 C D:TYR580 4.7 32.0 1.0 CB D:GLU526 4.8 36.5 1.0 C8 D:KQS888 4.8 36.6 1.0 CE1 D:TYR580 4.8 38.3 1.0 CA D:PHE581 5.0 34.4 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