Fluorine in PDB 6u65: Mcl-1 Bound to Compound 19

The structure of Mcl-1 Bound to Compound 19, PDB code: 6u65 was solved by J.A.Stuckey, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	43.12 / 2.09
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	69.712, 85.223, 109.753, 90.00, 90.00, 90.00
R / Rfree (%)	18.7 / 22.2

The binding sites of Fluorine atom in the Mcl-1 Bound to Compound 19 (pdb code 6u65). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 4 binding sites of Fluorine where determined in the Mcl-1 Bound to Compound 19, PDB code: 6u65:
Jump to Fluorine binding site number: 1; 2; 3; 4;

Fluorine binding site 1 out of 4 in the Mcl-1 Bound to Compound 19


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of Mcl-1 Bound to Compound 19 within 5.0Å range: probe atom residue distance (Å) B Occ A:F401 b:38.9 occ:1.00 F A:Q0A401 0.0 38.9 1.0 C9 A:Q0A401 1.4 37.8 1.0 C8 A:Q0A401 2.3 35.5 1.0 C10 A:Q0A401 2.4 36.6 1.0 CD1 A:LEU290 3.3 21.9 1.0 C7 A:Q0A401 3.6 31.6 1.0 C11 A:Q0A401 3.6 34.2 1.0 CG2 A:VAL274 3.7 20.6 1.0 CD1 A:ILE294 3.8 22.8 1.0 CA A:GLY271 3.9 16.7 1.0 CB A:VAL274 4.1 21.1 1.0 C6 A:Q0A401 4.1 29.0 1.0 CD2 A:PHE270 4.2 18.7 1.0 CG1 A:ILE294 4.2 20.6 1.0 CG A:LEU290 4.3 21.2 1.0 CD1 A:LEU246 4.4 33.6 1.0 CE2 A:PHE270 4.4 20.6 1.0 N A:GLY271 4.4 18.3 1.0 CG1 A:VAL274 4.4 21.8 1.0 CD2 A:LEU290 4.6 21.1 1.0 SD A:MET250 4.6 34.9 1.0 O A:PHE270 4.6 18.9 1.0 C A:PHE270 4.7 20.4 1.0

Fluorine binding site 2 out of 4 in the Mcl-1 Bound to Compound 19


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of Mcl-1 Bound to Compound 19 within 5.0Å range: probe atom residue distance (Å) B Occ B:F401 b:30.8 occ:1.00 F B:Q0A401 0.0 30.8 1.0 C9 B:Q0A401 1.4 26.6 1.0 C8 B:Q0A401 2.3 23.9 1.0 C10 B:Q0A401 2.3 25.7 1.0 CD1 B:LEU290 3.4 24.3 1.0 C7 B:Q0A401 3.6 19.9 1.0 C11 B:Q0A401 3.6 23.3 1.0 CA B:GLY271 3.7 18.4 1.0 CD1 B:ILE294 3.9 22.3 1.0 CG2 B:VAL274 4.0 21.0 1.0 C6 B:Q0A401 4.1 20.6 1.0 CD1 B:LEU246 4.1 26.7 1.0 CG1 B:ILE294 4.2 20.9 1.0 N B:GLY271 4.2 18.6 1.0 CD2 B:PHE270 4.3 19.4 1.0 CB B:VAL274 4.3 20.9 1.0 CG B:LEU290 4.4 23.4 1.0 CD2 B:LEU290 4.5 26.6 1.0 SD B:MET250 4.6 29.5 1.0 O B:PHE270 4.6 20.9 1.0 C B:PHE270 4.6 21.1 1.0 CG1 B:VAL274 4.7 20.2 1.0 CE2 B:PHE270 4.7 20.5 1.0 C B:GLY271 4.9 20.9 1.0 O B:GLY271 5.0 20.6 1.0 CB B:LEU246 5.0 22.7 1.0

Fluorine binding site 3 out of 4 in the Mcl-1 Bound to Compound 19


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of Mcl-1 Bound to Compound 19 within 5.0Å range: probe atom residue distance (Å) B Occ C:F401 b:33.1 occ:1.00 F C:Q0A401 0.0 33.1 1.0 C9 C:Q0A401 1.4 31.6 1.0 C10 C:Q0A401 2.4 30.6 1.0 C8 C:Q0A401 2.4 28.9 1.0 CD1 C:LEU290 3.4 35.0 1.0 C11 C:Q0A401 3.6 31.0 1.0 C7 C:Q0A401 3.6 29.6 1.0 CG2 C:VAL274 3.8 27.0 1.0 CA C:GLY271 3.9 24.4 1.0 CD1 C:ILE294 4.0 27.6 1.0 C6 C:Q0A401 4.1 31.1 1.0 CB C:VAL274 4.1 27.6 1.0 CD2 C:PHE270 4.3 29.3 1.0 CD1 C:LEU246 4.3 36.7 1.0 CG C:LEU290 4.3 33.4 1.0 N C:GLY271 4.3 24.8 1.0 CG1 C:ILE294 4.3 25.9 1.0 CD2 C:LEU290 4.5 34.0 1.0 SD C:MET250 4.5 39.8 1.0 CG1 C:VAL274 4.5 28.1 1.0 O C:PHE270 4.6 26.0 1.0 CE2 C:PHE270 4.6 31.2 1.0 C C:PHE270 4.7 27.3 1.0 C C:GLY271 4.9 27.8 1.0 O C:GLY271 4.9 27.9 1.0

Fluorine binding site 4 out of 4 in the Mcl-1 Bound to Compound 19


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 4 of Mcl-1 Bound to Compound 19 within 5.0Å range: probe atom residue distance (Å) B Occ D:F401 b:39.8 occ:1.00 F D:Q0A401 0.0 39.8 1.0 C9 D:Q0A401 1.4 37.7 1.0 C10 D:Q0A401 2.3 35.1 1.0 C8 D:Q0A401 2.3 37.8 1.0 CD1 D:LEU290 3.3 42.0 1.0 C11 D:Q0A401 3.6 35.3 1.0 C7 D:Q0A401 3.6 38.9 1.0 CA D:GLY271 3.7 27.0 1.0 CG2 D:VAL274 3.7 30.7 1.0 CB D:VAL274 3.9 32.0 1.0 CD1 D:LEU246 4.1 55.1 1.0 CD2 D:LEU290 4.1 42.5 1.0 C6 D:Q0A401 4.1 38.9 1.0 CG D:LEU290 4.2 41.9 1.0 CG1 D:VAL274 4.2 33.5 1.0 N D:GLY271 4.2 26.8 1.0 CE D:MET250 4.2 55.3 1.0 CD1 D:ILE294 4.3 30.5 1.0 CD2 D:PHE270 4.4 31.7 1.0 O D:PHE270 4.5 28.6 1.0 C D:PHE270 4.6 28.3 1.0 CG1 D:ILE294 4.7 35.1 1.0 CE2 D:PHE270 4.7 34.8 1.0 C D:GLY271 4.8 30.5 1.0 O D:GLY271 4.8 30.9 1.0 SD D:MET250 4.9 57.0 1.0 CB D:LEU246 5.0 52.1 1.0

K.J.Kump, L.Miao, A.S.A.Mady, N.H.Ansari, U.K.Shrestha, Y.Yang, M.Pal, C.Liao, A.Perdih, F.A.Abulwerdi, K.Chinnaswamy, J.L.Meagher, J.M.Carlson, M.Khanna, J.A.Stuckey, Z.Nikolovska-Coleska. Discovery and Characterization of 2,5-Substituted Benzoic Acid Dual Inhibitors of the Anti-Apoptotic Mcl-1 and Bfl-1 Proteins. J.Med.Chem. 2020.
ISSN: ISSN 0022-2623
PubMed: 31971799
DOI: 10.1021/ACS.JMEDCHEM.9B01442