Fluorine in PDB 6h6q: Fragment Derived Xiap Inhibitor

All present enzymatic activity of Fragment Derived Xiap Inhibitor:
2.3.2.27;

The structure of Fragment Derived Xiap Inhibitor, PDB code: 6h6q 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)	72.87 / 2.63
Space group	P 41 21 2
Cell size a, b, c (Å), α, β, γ (°)	99.491, 99.491, 107.043, 90.00, 90.00, 90.00
R / Rfree (%)	25.2 / 27.5

The structure of Fragment Derived Xiap Inhibitor also contains other interesting chemical elements:

Zinc

(Zn)

2 atoms

The binding sites of Fluorine atom in the Fragment Derived Xiap Inhibitor (pdb code 6h6q). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 2 binding sites of Fluorine where determined in the Fragment Derived Xiap Inhibitor, PDB code: 6h6q:
Jump to Fluorine binding site number: 1; 2;

Fluorine binding site 1 out of 2 in the Fragment Derived Xiap Inhibitor


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of Fragment Derived Xiap Inhibitor within 5.0Å range: probe atom residue distance (Å) B Occ A:F402 b:38.9 occ:0.89 F25 A:FUK402 0.0 38.9 0.9 C24 A:FUK402 1.4 38.5 0.9 C23 A:FUK402 2.3 35.6 0.9 C26 A:FUK402 2.4 38.5 0.9 H61 A:FUK402 2.5 36.4 0.9 H62 A:FUK402 2.5 38.5 0.9 CD1 A:LEU292 3.0 58.2 1.0 CD A:LYS299 3.4 56.2 1.0 O A:VAL298 3.4 49.9 1.0 C22 A:FUK402 3.6 36.4 0.9 CG A:LEU292 3.6 56.9 1.0 C27 A:FUK402 3.6 37.3 0.9 CE A:LYS299 3.8 80.8 1.0 CG A:LYS299 3.8 52.9 1.0 NZ A:LYS299 3.9 98.4 1.0 CB A:LYS299 3.9 47.3 1.0 CA A:GLY306 4.0 45.3 1.0 C A:VAL298 4.0 48.3 1.0 C21 A:FUK402 4.1 36.6 0.9 CD2 A:LEU292 4.2 58.4 1.0 H60 A:FUK402 4.4 37.0 0.9 H63 A:FUK402 4.4 37.3 0.9 CA A:LYS299 4.4 40.7 1.0 N A:LYS299 4.5 42.4 1.0 N A:VAL298 4.8 45.4 1.0 O A:HOH521 4.8 55.5 1.0 C A:GLY306 4.9 48.6 1.0 CB A:LYS297 4.9 50.8 1.0 CA A:VAL298 4.9 44.4 1.0 O A:HOH517 4.9 63.2 1.0 N A:GLY306 4.9 45.1 1.0 CB A:LEU292 5.0 54.7 1.0 O A:HOH529 5.0 54.6 1.0 N A:LEU307 5.0 46.9 1.0

Fluorine binding site 2 out of 2 in the Fragment Derived Xiap Inhibitor


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of Fragment Derived Xiap Inhibitor within 5.0Å range: probe atom residue distance (Å) B Occ B:F402 b:64.7 occ:0.92 F25 B:FUK402 0.0 64.7 0.9 C24 B:FUK402 1.4 58.9 0.9 C23 B:FUK402 2.3 55.6 0.9 C26 B:FUK402 2.3 59.9 0.9 H61 B:FUK402 2.5 55.6 0.9 H62 B:FUK402 2.5 60.1 0.9 CD1 B:LEU292 2.9 83.2 1.0 O B:VAL298 3.3 57.9 1.0 CG B:LEU292 3.4 80.4 1.0 CD B:LYS299 3.5 73.5 1.0 C22 B:FUK402 3.6 57.7 0.9 C27 B:FUK402 3.6 59.5 0.9 C B:VAL298 3.8 57.7 1.0 CB B:LYS299 3.8 49.9 1.0 CG B:LYS299 3.9 60.4 1.0 CE B:LYS299 4.0 97.7 1.0 CA B:GLY306 4.1 50.6 1.0 CD2 B:LEU292 4.1 83.3 1.0 C21 B:FUK402 4.1 58.3 0.9 NZ B:LYS299 4.1 0.3 1.0 N B:LYS299 4.3 48.3 1.0 CA B:LYS299 4.3 44.6 1.0 H60 B:FUK402 4.3 58.2 0.9 H63 B:FUK402 4.4 59.9 0.9 N B:VAL298 4.6 63.8 1.0 O B:HOH530 4.7 49.7 1.0 CA B:VAL298 4.7 60.3 1.0 CB B:LYS297 4.7 67.5 1.0 CB B:LEU292 4.7 76.2 1.0 C B:LYS297 4.9 68.8 1.0 C B:GLY306 4.9 54.3 1.0 N B:LEU307 4.9 51.4 1.0

C.N.Johnson, J.S.Ahn, I.M.Buck, E.Chiarparin, J.E.H.Day, A.Hopkins, S.Howard, E.J.Lewis, V.Martins, A.Millemaggi, J.M.Munck, L.W.Page, T.Peakman, M.Reader, S.J.Rich, G.Saxty, T.Smyth, N.T.Thompson, G.A.Ward, P.A.Williams, N.E.Wilsher, G.Chessari. A Fragment-Derived Clinical Candidate For Antagonism of X-Linked and Cellular Inhibitor of Apoptosis Proteins: 1-(6-[(4-Fluorophenyl)Methyl]-5-(Hydroxymethyl)-3, 3-Dimethyl-1 H,2 H,3 H-Pyrrolo[3,2- B]Pyridin-1-Yl)-2-[(2 R,5 R)-5-Methyl-2-([(3R)-3-Methylmorpholin-4-Yl]Methyl) Piperazin-1-Yl]Ethan-1-One (ASTX660). J. Med. Chem. V. 61 7314 2018.
ISSN: ISSN 1520-4804
PubMed: 30091600
DOI: 10.1021/ACS.JMEDCHEM.8B00900