Sodium in PDB 6h6r: 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: 6h6r 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)	29.56 / 2.03
Space group	P 41 2 2
Cell size a, b, c (Å), α, β, γ (°)	71.352, 71.352, 105.569, 90.00, 90.00, 90.00
R / Rfree (%)	21.2 / 24.3

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

Fluorine	(F)	1 atom
Zinc	(Zn)	1 atom

The binding sites of Sodium atom in the Fragment Derived Xiap Inhibitor (pdb code 6h6r). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total only one binding site of Sodium was determined in the Fragment Derived Xiap Inhibitor, PDB code: 6h6r:

Sodium binding site 1 out of 1 in the Fragment Derived Xiap Inhibitor


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Fragment Derived Xiap Inhibitor within 5.0Å range: probe atom residue distance (Å) B Occ A:Na402 b:75.7 occ:0.50 O A:HOH603 2.4 20.8 0.5 O A:HOH518 2.5 25.3 1.0 O A:PHE272 2.8 36.2 1.0 C A:PHE272 3.8 33.8 1.0 O A:HOH537 4.0 40.8 1.0 O A:THR274 4.4 33.4 1.0 N A:GLY273 4.5 31.0 1.0 CA A:GLY273 4.5 33.2 1.0 O A:THR271 4.5 34.0 1.0 O A:HOH513 4.6 31.2 1.0 CA A:PHE272 4.8 28.7 1.0 CA A:GLY293 4.9 32.1 1.0 C A:GLY273 4.9 36.6 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