Fluorine in PDB 5dda: Menin in Complex with Mi-333

The structure of Menin in Complex with Mi-333, PDB code: 5dda 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)	40.03 / 1.83
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	48.133, 79.998, 124.668, 90.00, 90.00, 90.00
R / Rfree (%)	16.4 / 21.1

The binding sites of Fluorine atom in the Menin in Complex with Mi-333 (pdb code 5dda). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 4 binding sites of Fluorine where determined in the Menin in Complex with Mi-333, PDB code: 5dda:
Jump to Fluorine binding site number: 1; 2; 3; 4;

Fluorine binding site 1 out of 4 in the Menin in Complex with Mi-333


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-333 within 5.0Å range: probe atom residue distance (Å) B Occ A:F601 b:27.2 occ:1.00 FAB A:59M601 0.0 27.2 1.0 CBA A:59M601 1.3 33.3 1.0 FAD A:59M601 2.2 29.1 1.0 FAC A:59M601 2.2 28.9 1.0 CAL A:59M601 2.4 25.1 1.0 O A:HOH905 3.0 50.4 1.0 C A:HIS181 3.1 24.1 1.0 N A:HIS181 3.1 18.5 1.0 CA A:HIS181 3.2 19.4 1.0 O A:HIS181 3.3 20.6 1.0 C A:ASP180 3.5 23.5 1.0 O A:HOH914 3.6 42.5 1.0 N A:ALA182 3.6 21.1 1.0 CAS A:59M601 3.7 23.9 1.0 CB A:SER155 3.8 25.7 1.0 O A:ASP180 3.8 21.9 1.0 CB A:ALA182 4.0 19.5 1.0 O A:HOH708 4.0 32.2 1.0 CA A:ASP180 4.4 19.1 1.0 OG A:SER155 4.4 21.8 1.0 CA A:ALA182 4.4 16.7 1.0 SAR A:59M601 4.6 25.1 0.9 O A:HOH829 4.6 33.5 1.0 CAF A:59M601 4.6 24.4 1.0 CB A:HIS181 4.7 20.0 1.0 N A:ASP180 4.8 18.7 1.0 CA A:SER155 4.9 22.8 1.0 O A:SER178 4.9 21.9 1.0

Fluorine binding site 2 out of 4 in the Menin in Complex with Mi-333


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-333 within 5.0Å range: probe atom residue distance (Å) B Occ A:F601 b:28.9 occ:1.00 FAC A:59M601 0.0 28.9 1.0 CBA A:59M601 1.3 33.3 1.0 FAD A:59M601 2.2 29.1 1.0 FAB A:59M601 2.2 27.2 1.0 CAL A:59M601 2.4 25.1 1.0 CAS A:59M601 2.9 23.9 1.0 SAR A:59M601 3.2 25.1 0.9 CB A:SER155 3.3 25.7 1.0 CD2 A:LEU177 3.4 22.7 1.0 CE1 A:PHE238 3.6 22.4 1.0 OG A:SER155 3.7 21.8 1.0 CB A:ALA182 3.8 19.5 1.0 O A:HIS181 3.9 20.6 1.0 CAF A:59M601 4.1 24.4 1.0 CZ A:PHE238 4.1 23.2 1.0 C A:HIS181 4.2 24.1 1.0 C2 A:DMS602 4.4 36.0 0.5 C4 A:59M601 4.5 25.9 1.0 S A:DMS602 4.5 38.5 0.5 N A:ALA182 4.5 21.1 1.0 C1 A:DMS607 4.5 44.0 0.5 CA A:ALA182 4.6 16.7 1.0 CD1 A:PHE238 4.6 24.9 1.0 CA A:SER155 4.7 22.8 1.0 CG A:LEU177 4.7 23.4 1.0 O A:HOH905 4.7 50.4 1.0 C5 A:59M601 4.8 32.1 1.0 N A:HIS181 4.9 18.5 1.0 CA A:HIS181 4.9 19.4 1.0 CB A:LEU177 5.0 20.4 1.0 O A:SER178 5.0 21.9 1.0 O A:HOH914 5.0 42.5 1.0

Fluorine binding site 3 out of 4 in the Menin in Complex with Mi-333


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-333 within 5.0Å range: probe atom residue distance (Å) B Occ A:F601 b:29.1 occ:1.00 FAD A:59M601 0.0 29.1 1.0 CBA A:59M601 1.3 33.3 1.0 FAC A:59M601 2.2 28.9 1.0 FAB A:59M601 2.2 27.2 1.0 CAL A:59M601 2.4 25.1 1.0 CAS A:59M601 2.9 23.9 1.0 O A:HOH914 3.2 42.5 1.0 C2 A:DMS602 3.4 36.0 0.5 CAF A:59M601 3.4 24.4 1.0 OG A:SER155 3.4 21.8 1.0 CB A:SER155 3.6 25.7 1.0 O A:HOH905 3.6 50.4 1.0 S A:DMS602 3.7 38.5 0.5 O A:DMS607 3.8 54.3 0.5 SAR A:59M601 3.9 25.1 0.9 O A:HOH829 3.9 33.5 1.0 C1 A:DMS607 4.0 44.0 0.5 C5 A:59M601 4.4 32.1 1.0 S A:DMS607 4.6 56.6 0.5 O A:DMS602 4.6 51.8 0.5 C4 A:59M601 4.7 25.9 1.0 CE1 A:PHE238 4.7 22.4 1.0 N A:HIS181 4.9 18.5 1.0 C A:ASP180 5.0 23.5 1.0

Fluorine binding site 4 out of 4 in the Menin in Complex with Mi-333


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 4 of Menin in Complex with Mi-333 within 5.0Å range: probe atom residue distance (Å) B Occ A:F601 b:53.1 occ:1.00 FAA A:59M601 0.0 53.1 1.0 CAG A:59M601 1.3 39.7 1.0 CAT A:59M601 2.3 35.0 1.0 SAQ A:59M601 3.0 31.8 0.8 CB A:MET322 3.2 21.0 0.5 CB A:MET322 3.3 23.3 0.5 NAO A:59M601 3.5 46.6 0.9 CD1 A:TYR319 3.7 26.9 1.0 C A:MET322 3.7 26.9 1.0 N A:TYR323 3.9 21.9 1.0 O A:MET322 4.1 22.8 1.0 CA A:MET322 4.1 20.2 0.5 CA A:MET322 4.2 21.8 0.5 CE1 A:TYR319 4.2 30.4 1.0 CG A:MET322 4.2 41.7 0.5 CAU A:59M601 4.2 44.5 1.0 CG A:MET322 4.3 29.0 0.5 NAP A:59M601 4.3 38.4 0.9 CA A:TYR323 4.4 20.1 1.0 CG A:TYR319 4.4 20.9 1.0 O A:TYR319 4.5 23.9 1.0 SD A:MET322 4.5 26.4 0.3 O A:HOH918 4.6 45.4 1.0 CG A:TYR323 4.7 20.7 1.0 CB A:TYR319 4.7 19.2 1.0 O A:HOH843 4.8 33.3 1.0 CD1 A:TYR323 4.8 22.8 1.0 CD2 A:TYR323 4.8 26.6 1.0 CA A:TYR319 4.9 18.6 1.0 SD A:MET322 4.9 31.0 0.7 O A:HOH856 4.9 40.2 1.0 OE2 A:GLU363 4.9 65.0 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