Fluorine in PDB 5ddf: Menin in Complex with Mi-273

The structure of Menin in Complex with Mi-273, PDB code: 5ddf 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)	49.34 / 1.66
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	48.553, 80.189, 124.989, 90.00, 90.00, 90.00
R / Rfree (%)	15.8 / 18.8

The binding sites of Fluorine atom in the Menin in Complex with Mi-273 (pdb code 5ddf). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 5 binding sites of Fluorine where determined in the Menin in Complex with Mi-273, PDB code: 5ddf:
Jump to Fluorine binding site number: 1; 2; 3; 4; 5;

Fluorine binding site 1 out of 5 in the Menin in Complex with Mi-273


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-273 within 5.0Å range: probe atom residue distance (Å) B Occ A:F601 b:21.0 occ:0.90 FAC A:5A1601 0.0 21.0 0.9 CBB A:5A1601 1.3 17.9 0.8 FAE A:5A1601 2.2 27.9 0.9 FAD A:5A1601 2.2 26.1 0.9 CBC A:5A1601 2.3 24.7 0.9 FAG A:5A1601 2.6 34.6 0.9 O A:HOH1068 2.6 39.8 1.0 FAF A:5A1601 2.7 38.5 0.9 C A:HIS181 3.1 9.8 1.0 N A:HIS181 3.1 9.6 1.0 CA A:HIS181 3.2 8.0 1.0 C A:ASP180 3.5 12.3 1.0 O A:HIS181 3.5 9.1 1.0 N A:ALA182 3.6 6.8 1.0 CAU A:5A1601 3.7 15.3 0.9 O A:HOH1037 3.7 35.2 1.0 O A:ASP180 3.8 11.9 1.0 CB A:SER155 3.9 11.3 1.0 O A:HOH723 4.1 22.6 1.0 CB A:ALA182 4.2 9.5 1.0 CA A:ASP180 4.3 11.8 1.0 CA A:ALA182 4.5 6.7 1.0 OG A:SER155 4.5 12.7 1.0 SAS A:5A1601 4.6 19.5 0.9 CAI A:5A1601 4.6 19.5 0.9 CB A:HIS181 4.7 9.7 1.0 O A:HOH895 4.7 19.6 1.0 N A:ASP180 4.8 9.4 1.0 CA A:SER155 5.0 10.0 1.0

Fluorine binding site 2 out of 5 in the Menin in Complex with Mi-273


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-273 within 5.0Å range: probe atom residue distance (Å) B Occ A:F601 b:26.1 occ:0.90 FAD A:5A1601 0.0 26.1 0.9 CBB A:5A1601 1.3 17.9 0.8 FAE A:5A1601 2.2 27.9 0.9 FAC A:5A1601 2.2 21.0 0.9 CBC A:5A1601 2.3 24.7 0.9 FAF A:5A1601 2.6 38.5 0.9 CAU A:5A1601 3.0 15.3 0.9 CB A:SER155 3.1 11.3 1.0 SAS A:5A1601 3.3 19.5 0.9 FAG A:5A1601 3.4 34.6 0.9 OG A:SER155 3.5 12.7 1.0 CE1 A:PHE238 3.7 10.1 1.0 CD2 A:LEU177 3.7 12.0 1.0 CB A:ALA182 4.0 9.5 1.0 CAI A:5A1601 4.1 19.5 0.9 CZ A:PHE238 4.1 10.7 1.0 O A:HOH1068 4.2 39.8 1.0 O A:HIS181 4.3 9.1 1.0 C A:HIS181 4.3 9.8 1.0 CA A:SER155 4.5 10.0 1.0 C4 A:5A1601 4.6 18.5 0.9 N A:ALA182 4.6 6.8 1.0 S A:DMS608 4.7 29.0 0.6 CA A:ALA182 4.8 6.7 1.0 CD1 A:PHE238 4.8 10.9 1.0 C2 A:DMS608 4.9 20.6 0.6 C5 A:5A1601 4.9 20.0 0.9 CG A:LEU177 5.0 9.2 1.0 CA A:HIS181 5.0 8.0 1.0 N A:HIS181 5.0 9.6 1.0

Fluorine binding site 3 out of 5 in the Menin in Complex with Mi-273


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-273 within 5.0Å range: probe atom residue distance (Å) B Occ A:F601 b:27.9 occ:0.90 FAE A:5A1601 0.0 27.9 0.9 CBB A:5A1601 1.3 17.9 0.8 FAC A:5A1601 2.2 21.0 0.9 FAD A:5A1601 2.2 26.1 0.9 CBC A:5A1601 2.3 24.7 0.9 FAG A:5A1601 2.7 34.6 0.9 CAU A:5A1601 2.9 15.3 0.9 O A:HOH1068 3.2 39.8 1.0 CAI A:5A1601 3.4 19.5 0.9 O A:HOH1037 3.4 35.2 1.0 FAF A:5A1601 3.4 38.5 0.9 OG A:SER155 3.6 12.7 1.0 CB A:SER155 3.8 11.3 1.0 SAS A:5A1601 4.0 19.5 0.9 O A:HOH895 4.0 19.6 1.0 S A:DMS608 4.2 29.0 0.6 C5 A:5A1601 4.4 20.0 0.9 C2 A:DMS608 4.5 20.6 0.6 C4 A:5A1601 4.7 18.5 0.9 C A:ASP180 4.9 12.3 1.0 O A:DMS608 4.9 38.5 0.6 N A:HIS181 4.9 9.6 1.0

Fluorine binding site 4 out of 5 in the Menin in Complex with Mi-273


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-273 within 5.0Å range: probe atom residue distance (Å) B Occ A:F601 b:38.5 occ:0.90 FAF A:5A1601 0.0 38.5 0.9 CBC A:5A1601 1.3 24.7 0.9 FAG A:5A1601 2.1 34.6 0.9 CAU A:5A1601 2.3 15.3 0.9 CBB A:5A1601 2.3 17.9 0.8 FAD A:5A1601 2.6 26.1 0.9 FAC A:5A1601 2.7 21.0 0.9 SAS A:5A1601 2.7 19.5 0.9 O A:SER178 2.8 11.5 1.0 O A:HIS181 3.1 9.1 1.0 FAE A:5A1601 3.4 27.9 0.9 CAI A:5A1601 3.5 19.5 0.9 C A:HIS181 3.7 9.8 1.0 N A:HIS181 3.7 9.6 1.0 C A:SER178 3.8 8.3 1.0 CD2 A:LEU177 3.8 12.0 1.0 N A:SER178 4.0 7.3 1.0 CB A:LEU177 4.0 8.1 1.0 C4 A:5A1601 4.2 18.5 0.9 N A:ASP180 4.2 9.4 1.0 C A:GLU179 4.2 10.5 1.0 CA A:HIS181 4.2 8.0 1.0 CA A:LEU177 4.3 7.8 1.0 C A:ASP180 4.4 12.3 1.0 C5 A:5A1601 4.4 20.0 0.9 C A:LEU177 4.5 8.3 1.0 CG A:LEU177 4.5 9.2 1.0 O A:GLU179 4.5 10.8 1.0 CA A:SER178 4.5 7.3 1.0 N A:ALA182 4.6 6.8 1.0 N A:GLU179 4.6 6.8 1.0 CA A:ASP180 4.6 11.8 1.0 CA A:GLU179 4.6 7.6 1.0 CE A:MET278 4.7 25.6 1.0 CB A:ALA182 5.0 9.5 1.0 CA A:ALA182 5.0 6.7 1.0 OG A:SER178 5.0 9.8 1.0

Fluorine binding site 5 out of 5 in the Menin in Complex with Mi-273


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 5 of Menin in Complex with Mi-273 within 5.0Å range: probe atom residue distance (Å) B Occ A:F601 b:34.6 occ:0.90 FAG A:5A1601 0.0 34.6 0.9 CBC A:5A1601 1.3 24.7 0.9 FAF A:5A1601 2.1 38.5 0.9 CAU A:5A1601 2.3 15.3 0.9 CBB A:5A1601 2.3 17.9 0.8 FAC A:5A1601 2.6 21.0 0.9 FAE A:5A1601 2.7 27.9 0.9 CAI A:5A1601 2.8 19.5 0.9 O A:GLU179 3.0 10.8 1.0 C A:GLU179 3.1 10.5 1.0 N A:ASP180 3.2 9.4 1.0 CA A:ASP180 3.2 11.8 1.0 N A:HIS181 3.4 9.6 1.0 C A:ASP180 3.4 12.3 1.0 FAD A:5A1601 3.4 26.1 0.9 O A:HOH1037 3.6 35.2 1.0 SAS A:5A1601 3.6 19.5 0.9 O A:SER178 3.7 11.5 1.0 C5 A:5A1601 4.1 20.0 0.9 CA A:GLU179 4.1 7.6 1.0 O A:ASP180 4.2 11.9 1.0 O A:HIS181 4.3 9.1 1.0 CA A:HIS181 4.4 8.0 1.0 C A:SER178 4.4 8.3 1.0 C4 A:5A1601 4.5 18.5 0.9 C A:HIS181 4.5 9.8 1.0 O A:HOH1068 4.6 39.8 1.0 N A:GLU179 4.6 6.8 1.0 O A:HOH832 4.6 20.2 1.0 CB A:ASP180 4.7 12.7 1.0 CAL A:5A1601 4.8 16.9 0.9

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