Fluorine in PDB 5dd9: Menin in Complex with Mi-326

The structure of Menin in Complex with Mi-326, PDB code: 5dd9 was solved by J.Pollock, B.Dmitry, T.Cierpicki, J.Grembecka, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	39.61 / 1.62
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	48.830, 80.230, 125.228, 90.00, 90.00, 90.00
R / Rfree (%)	16.2 / 19.5

The binding sites of Fluorine atom in the Menin in Complex with Mi-326 (pdb code 5dd9). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 3 binding sites of Fluorine where determined in the Menin in Complex with Mi-326, PDB code: 5dd9:
Jump to Fluorine binding site number: 1; 2; 3;

Fluorine binding site 1 out of 3 in the Menin in Complex with Mi-326


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of Menin in Complex with Mi-326 within 5.0Å range: probe atom residue distance (Å) B Occ A:F601 b:14.9 occ:1.00 FAB A:59K601 0.0 14.9 1.0 CAZ A:59K601 1.3 13.9 1.0 FAD A:59K601 2.2 14.2 1.0 FAC A:59K601 2.2 16.9 1.0 CAK A:59K601 2.4 11.6 1.0 CAS A:59K601 2.9 12.8 1.0 SAQ A:59K601 3.2 13.3 1.0 CB A:SER155 3.3 14.0 1.0 CD2 A:LEU177 3.6 12.5 1.0 CE1 A:PHE238 3.7 13.4 1.0 O A:HIS181 3.8 12.3 1.0 CB A:ALA182 3.8 11.4 1.0 OG A:SER155 3.8 15.2 1.0 CAF A:59K601 4.0 14.8 1.0 C A:HIS181 4.1 13.2 1.0 CZ A:PHE238 4.2 13.9 1.0 C1 A:DMS607 4.2 23.4 0.5 N A:ALA182 4.4 11.4 1.0 S A:DMS602 4.4 22.1 0.5 C4 A:59K601 4.5 13.7 1.0 CA A:ALA182 4.5 9.8 1.0 C2 A:DMS602 4.6 26.2 0.5 CD1 A:PHE238 4.7 14.2 1.0 N A:HIS181 4.7 9.9 1.0 CA A:SER155 4.7 13.1 1.0 CA A:HIS181 4.8 11.0 1.0 CG A:LEU177 4.8 12.8 1.0 C5 A:59K601 4.8 12.0 1.0 O A:SER178 4.9 11.3 1.0 O A:HOH1016 5.0 37.2 1.0

Fluorine binding site 2 out of 3 in the Menin in Complex with Mi-326


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of Menin in Complex with Mi-326 within 5.0Å range: probe atom residue distance (Å) B Occ A:F601 b:16.9 occ:1.00 FAC A:59K601 0.0 16.9 1.0 CAZ A:59K601 1.3 13.9 1.0 FAB A:59K601 2.2 14.9 1.0 FAD A:59K601 2.2 14.2 1.0 CAK A:59K601 2.4 11.6 1.0 CAS A:59K601 2.8 12.8 1.0 O A:HOH1073 3.2 34.7 1.0 C1 A:DMS607 3.3 23.4 0.5 CAF A:59K601 3.3 14.8 1.0 OG A:SER155 3.5 15.2 1.0 O A:HOH996 3.6 45.6 1.0 CB A:SER155 3.6 14.0 1.0 S A:DMS602 3.7 22.1 0.5 O A:HOH1016 3.8 37.2 1.0 C2 A:DMS602 3.9 26.2 0.5 SAQ A:59K601 4.0 13.3 1.0 O A:HOH829 4.1 23.8 1.0 O A:DMS602 4.1 24.8 0.5 C5 A:59K601 4.4 12.0 1.0 C4 A:59K601 4.7 13.7 1.0 N A:HIS181 4.8 9.9 1.0 CE1 A:PHE238 4.8 13.4 1.0 S A:DMS607 4.8 32.0 0.5 C A:ASP180 4.9 12.0 1.0

Fluorine binding site 3 out of 3 in the Menin in Complex with Mi-326


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of Menin in Complex with Mi-326 within 5.0Å range: probe atom residue distance (Å) B Occ A:F601 b:14.2 occ:1.00 FAD A:59K601 0.0 14.2 1.0 CAZ A:59K601 1.3 13.9 1.0 FAB A:59K601 2.2 14.9 1.0 FAC A:59K601 2.2 16.9 1.0 CAK A:59K601 2.4 11.6 1.0 C A:HIS181 3.0 13.2 1.0 CA A:HIS181 3.0 11.0 1.0 N A:HIS181 3.0 9.9 1.0 O A:HIS181 3.2 12.3 1.0 O A:HOH1016 3.2 37.2 1.0 C A:ASP180 3.5 12.0 1.0 N A:ALA182 3.5 11.4 1.0 CAS A:59K601 3.7 12.8 1.0 O A:ASP180 3.8 12.8 1.0 CB A:SER155 3.8 14.0 1.0 O A:HOH1073 3.8 34.7 1.0 O A:HOH752 3.9 26.9 1.0 CB A:ALA182 4.1 11.4 1.0 CA A:ALA182 4.3 9.8 1.0 OG A:SER155 4.4 15.2 1.0 CA A:ASP180 4.4 12.7 1.0 CB A:HIS181 4.6 13.2 1.0 CAF A:59K601 4.7 14.8 1.0 SAQ A:59K601 4.7 13.3 1.0 O A:HOH829 4.8 23.8 1.0 CA A:SER155 4.9 13.1 1.0 N A:ASP180 4.9 10.9 1.0 O A:SER178 5.0 11.3 1.0

J.Pollock, D.Borkin, G.Lund, T.Purohit, E.Dyguda-Kazimierowicz, J.Grembecka, T.Cierpicki. Rational Design of Orthogonal Multipolar Interactions with Fluorine in Protein-Ligand Complexes. J.Med.Chem. V. 58 7465 2015.
ISSN: ISSN 0022-2623
PubMed: 26288158
DOI: 10.1021/ACS.JMEDCHEM.5B00975