Fluorine in PDB 6ud2: Co-Crystal Structure of Compound 1 Bound to Human Mcl-1

The structure of Co-Crystal Structure of Compound 1 Bound to Human Mcl-1, PDB code: 6ud2 was solved by X.Huang, D.Whittington, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	44.88 / 1.70
Space group	C 2 2 21
Cell size a, b, c (Å), α, β, γ (°)	44.028, 89.768, 84.855, 90.00, 90.00, 90.00
R / Rfree (%)	20 / 23.9

The structure of Co-Crystal Structure of Compound 1 Bound to Human Mcl-1 also contains other interesting chemical elements:

Chlorine

(Cl)

1 atom

The binding sites of Fluorine atom in the Co-Crystal Structure of Compound 1 Bound to Human Mcl-1 (pdb code 6ud2). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 2 binding sites of Fluorine where determined in the Co-Crystal Structure of Compound 1 Bound to Human Mcl-1, PDB code: 6ud2:
Jump to Fluorine binding site number: 1; 2;

Fluorine binding site 1 out of 2 in the Co-Crystal Structure of Compound 1 Bound to Human Mcl-1


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of Co-Crystal Structure of Compound 1 Bound to Human Mcl-1 within 5.0Å range: probe atom residue distance (Å) B Occ A:F401 b:36.6 occ:1.00 F1 A:Q4D401 0.0 36.6 1.0 C37 A:Q4D401 1.3 34.3 1.0 F2 A:Q4D401 2.2 39.4 1.0 C36 A:Q4D401 2.4 30.9 1.0 C38 A:Q4D401 2.4 31.8 1.0 C A:GLY230 3.1 22.7 1.0 N5 A:Q4D401 3.2 27.4 1.0 CA A:GLY230 3.2 22.5 1.0 N A:MET231 3.4 21.4 1.0 O A:GLY230 3.5 22.5 1.0 O A:HOH505 3.9 34.9 1.0 O A:ALA227 4.1 16.5 1.0 C35 A:Q4D401 4.1 25.9 1.0 CA A:MET231 4.2 21.9 1.0 N A:GLY230 4.4 20.3 1.0 CA A:ALA227 4.9 15.7 1.0 CB A:MET231 4.9 21.8 1.0 C A:ALA227 4.9 15.1 1.0

Fluorine binding site 2 out of 2 in the Co-Crystal Structure of Compound 1 Bound to Human Mcl-1


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of Co-Crystal Structure of Compound 1 Bound to Human Mcl-1 within 5.0Å range: probe atom residue distance (Å) B Occ A:F401 b:39.4 occ:1.00 F2 A:Q4D401 0.0 39.4 1.0 C37 A:Q4D401 1.3 34.3 1.0 F1 A:Q4D401 2.2 36.6 1.0 C36 A:Q4D401 2.4 30.9 1.0 C38 A:Q4D401 2.4 31.8 1.0 N5 A:Q4D401 2.8 27.4 1.0 CD A:LYS234 3.8 39.0 1.0 O A:HOH513 3.8 46.3 1.0 O A:GLY230 4.0 22.5 1.0 CA A:MET231 4.0 21.9 1.0 N A:MET231 4.0 21.4 1.0 C A:GLY230 4.0 22.7 1.0 CE A:MET231 4.2 31.0 1.0 C35 A:Q4D401 4.3 25.9 1.0 SD A:MET231 4.4 30.8 1.0 CB A:LYS234 4.4 30.8 1.0 O A:HOH505 4.4 34.9 1.0 CB A:MET231 4.6 21.8 1.0 CG A:LYS234 4.6 35.7 1.0 CA A:GLY230 4.8 22.5 1.0 NZ A:LYS234 4.9 46.9 1.0 CE A:LYS234 4.9 43.0 1.0

G.Rescourio, A.Z.Gonzalez, S.Jabri, B.Belmontes, G.Moody, D.Whittington, X.Huang, S.Caenepeel, M.Cardozo, A.C.Cheng, D.Chow, H.Dou, A.Jones, R.C.Kelly, Y.Li, M.Lizarzaburu, M.C.Lo, R.Mallari, C.Meleza, Y.Rew, S.Simonovich, D.Sun, S.Turcotte, X.Yan, S.G.Wong, E.Yanez, M.Zancanella, J.Houze, J.C.Medina, P.E.Hughes, S.P.Brown. Discovery and in Vivo Evaluation of Macrocyclic Mcl-1 Inhibitors Featuring An Alpha-Hydroxy Phenylacetic Acid Pharmacophore or Bioisostere. J.Med.Chem. 2019.
ISSN: ISSN 0022-2623
PubMed: 31736296
DOI: 10.1021/ACS.JMEDCHEM.9B01310