Zinc 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:

Fluorine

(F)

2 atoms

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

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


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Fragment Derived Xiap Inhibitor within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn401 b:43.8 occ:1.00 NE2 A:HIS320 2.2 36.3 1.0 SG A:CYS300 2.2 39.4 1.0 SG A:CYS327 2.3 39.5 1.0 SG A:CYS303 2.4 39.8 1.0 CB A:CYS327 3.0 34.2 1.0 CB A:CYS303 3.1 37.3 1.0 CB A:CYS300 3.1 35.8 1.0 CE1 A:HIS320 3.1 37.2 1.0 CD2 A:HIS320 3.3 35.7 1.0 N A:CYS303 3.5 38.7 1.0 CA A:CYS303 3.9 38.0 1.0 ND1 A:HIS320 4.3 37.2 1.0 CA A:CYS327 4.3 32.7 1.0 CG A:HIS320 4.4 34.8 1.0 CB A:HIS302 4.5 31.5 1.0 CA A:CYS300 4.6 36.3 1.0 C A:HIS302 4.6 42.4 1.0 CB A:TYR324 4.7 37.8 1.0 C A:CYS303 4.8 39.9 1.0 CB A:TYR329 4.9 30.7 1.0 N A:HIS302 4.9 34.9 1.0 CA A:HIS302 4.9 33.5 1.0 N A:GLY304 5.0 34.7 1.0

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


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Fragment Derived Xiap Inhibitor within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn401 b:45.5 occ:1.00 NE2 B:HIS320 2.2 41.2 1.0 SG B:CYS300 2.2 41.8 1.0 SG B:CYS303 2.3 45.2 1.0 SG B:CYS327 2.4 44.7 1.0 CB B:CYS300 3.0 38.5 1.0 CB B:CYS327 3.1 39.9 1.0 CB B:CYS303 3.1 42.0 1.0 CE1 B:HIS320 3.1 42.1 1.0 CD2 B:HIS320 3.3 40.7 1.0 N B:CYS303 3.5 42.1 1.0 CA B:CYS303 3.9 42.3 1.0 ND1 B:HIS320 4.3 43.8 1.0 CG B:HIS320 4.4 41.6 1.0 CA B:CYS327 4.4 40.1 1.0 CA B:CYS300 4.5 39.9 1.0 CB B:HIS302 4.6 39.4 1.0 C B:HIS302 4.6 46.0 1.0 CB B:TYR324 4.7 36.0 1.0 C B:CYS303 4.8 50.9 1.0 N B:GLY304 4.9 47.0 1.0 N B:HIS302 4.9 41.9 1.0 CA B:HIS302 4.9 40.8 1.0 CB B:TYR329 5.0 41.1 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