Fluorine in PDB 5oqw: Xiap in Complex with Small Molecule

All present enzymatic activity of Xiap in Complex with Small Molecule:
2.3.2.27;

The structure of Xiap in Complex with Small Molecule, PDB code: 5oqw was solved by P.A.Williams, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	72.84 / 2.31
Space group	P 41 21 2
Cell size a, b, c (Å), α, β, γ (°)	99.380, 99.380, 106.733, 90.00, 90.00, 90.00
R / Rfree (%)	21.3 / 24.6

The structure of Xiap in Complex with Small Molecule also contains other interesting chemical elements:

Zinc	(Zn)	2 atoms
Sodium	(Na)	1 atom

The binding sites of Fluorine atom in the Xiap in Complex with Small Molecule (pdb code 5oqw). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 2 binding sites of Fluorine where determined in the Xiap in Complex with Small Molecule, PDB code: 5oqw:
Jump to Fluorine binding site number: 1; 2;

Fluorine binding site 1 out of 2 in the Xiap in Complex with Small Molecule


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of Xiap in Complex with Small Molecule within 5.0Å range: probe atom residue distance (Å) B Occ A:F403 b:59.2 occ:1.00 F24 A:A4E403 0.0 59.2 1.0 C23 A:A4E403 1.4 52.7 1.0 C25 A:A4E403 2.3 51.7 1.0 C22 A:A4E403 2.3 49.1 1.0 H63 A:A4E403 2.5 50.4 1.0 H62 A:A4E403 2.5 50.5 1.0 CG A:LYS299 3.0 54.5 1.0 CD1 A:LEU292 3.2 57.9 1.0 CG A:LEU292 3.4 53.0 1.0 CD A:LYS299 3.4 59.0 1.0 O A:VAL298 3.6 43.3 1.0 C21 A:A4E403 3.6 48.5 1.0 C26 A:A4E403 3.6 50.6 1.0 CD2 A:LEU292 3.9 52.1 1.0 CB A:LYS297 4.0 49.1 1.0 C A:VAL298 4.0 42.3 1.0 C20 A:A4E403 4.1 50.8 1.0 CA A:GLY306 4.2 43.4 1.0 H61 A:A4E403 4.4 50.2 1.0 H64 A:A4E403 4.4 51.2 1.0 N A:VAL298 4.4 42.9 1.0 CB A:LYS299 4.4 48.1 1.0 CD A:LYS297 4.5 59.0 1.0 CE A:LYS299 4.5 60.7 1.0 C A:LYS297 4.6 44.4 1.0 N A:LYS299 4.6 41.4 1.0 CG A:LYS297 4.6 54.6 1.0 CA A:VAL298 4.7 42.9 1.0 CA A:LYS297 4.7 47.2 1.0 CB A:LEU292 4.8 53.9 1.0 CA A:LYS299 4.9 44.7 1.0 N A:LEU307 4.9 45.1 1.0

Fluorine binding site 2 out of 2 in the Xiap in Complex with Small Molecule


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of Xiap in Complex with Small Molecule within 5.0Å range: probe atom residue distance (Å) B Occ B:F402 b:52.9 occ:1.00 F24 B:A4E402 0.0 52.9 1.0 C23 B:A4E402 1.4 54.8 1.0 C25 B:A4E402 2.3 57.6 1.0 C22 B:A4E402 2.3 54.3 1.0 H63 B:A4E402 2.5 55.5 1.0 H62 B:A4E402 2.5 52.5 1.0 CG B:LYS299 3.3 59.3 1.0 C26 B:A4E402 3.6 57.4 1.0 C21 B:A4E402 3.6 51.0 1.0 O B:VAL298 3.6 45.0 1.0 CD2 B:LEU292 3.7 61.4 1.0 CB B:LYS297 3.8 57.8 1.0 CD B:LYS299 3.9 65.7 1.0 CD1 B:LEU292 4.0 56.1 1.0 CB B:LEU292 4.0 55.0 1.0 C B:VAL298 4.1 47.7 1.0 CG B:LEU292 4.1 59.2 1.0 C20 B:A4E402 4.1 51.9 1.0 N B:VAL298 4.2 49.2 1.0 H64 B:A4E402 4.4 55.2 1.0 H61 B:A4E402 4.4 52.9 1.0 CA B:GLY306 4.4 48.9 1.0 C B:LYS297 4.4 52.2 1.0 CG B:LYS297 4.4 63.0 1.0 O B:HOH604 4.5 58.8 1.0 CA B:LYS297 4.5 54.7 1.0 CD B:LYS297 4.5 68.1 1.0 CA B:VAL298 4.6 47.7 1.0 CB B:LYS299 4.6 52.1 1.0 N B:LYS299 4.6 49.4 1.0 NZ B:LYS299 4.7 82.2 1.0 O B:HOH535 4.7 64.7 1.0 O B:HOH578 4.8 70.9 1.0 CE B:LYS299 4.9 73.9 1.0 O B:LYS297 4.9 53.0 1.0 CA B:LYS299 4.9 47.6 1.0 N B:LEU307 5.0 45.9 1.0

G.A.Ward, E.J.Lewis, J.S.Ahn, C.N.Johnson, J.F.Lyons, V.Martins, J.M.Munck, S.J.Rich, T.Smyth, N.T.Thompson, P.A.Williams, N.E.Wilsher, N.G.Wallis, G.Chessari. ASTX660, A Novel Non-Peptidomimetic Antagonist of CIAP1/2 and Xiap, Potently Induces Tnf Alpha-Dependent Apoptosis in Cancer Cell Lines and Inhibits Tumor Growth. Mol. Cancer Ther. V. 17 1381 2018.
ISSN: ESSN 1538-8514
PubMed: 29695633
DOI: 10.1158/1535-7163.MCT-17-0848