Fluorine in PDB 5dde: Menin in Complex with Mi-859

The structure of Menin in Complex with Mi-859, PDB code: 5dde 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)	41.60 / 1.78
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	48.705, 79.713, 124.644, 90.00, 90.00, 90.00
R / Rfree (%)	17.1 / 19.9

The binding sites of Fluorine atom in the Menin in Complex with Mi-859 (pdb code 5dde). 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-859, PDB code: 5dde:
Jump to Fluorine binding site number: 1; 2; 3; 4;

Fluorine binding site 1 out of 4 in the Menin in Complex with Mi-859


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-859 within 5.0Å range: probe atom residue distance (Å) B Occ A:F601 b:14.1 occ:0.60 FAC A:5A0601 0.0 14.1 0.6 FAD A:5A0602 0.1 21.0 0.4 CAW A:5A0602 1.4 20.1 0.4 CAW A:5A0601 1.4 12.8 0.6 FAD A:5A0601 2.3 15.8 0.6 FAC A:5A0602 2.3 17.2 0.4 CAL A:5A0602 2.4 21.3 0.4 CAL A:5A0601 2.4 11.9 0.6 CAS A:5A0602 2.9 23.3 0.4 CAS A:5A0601 2.9 10.9 0.6 SAQ A:5A0602 3.1 25.6 0.4 SAQ A:5A0601 3.1 10.4 0.6 CB A:SER155 3.3 12.6 1.0 CD2 A:LEU177 3.3 12.1 1.0 CE1 A:PHE238 3.4 13.6 1.0 CB A:ALA182 3.8 12.6 1.0 OG A:SER155 3.8 13.3 1.0 C1 A:DMS608 3.9 21.9 0.4 O A:HIS181 4.0 12.6 1.0 CAF A:5A0602 4.0 25.4 0.4 CZ A:PHE238 4.0 13.5 1.0 CAF A:5A0601 4.1 11.0 0.6 S A:DMS607 4.2 23.1 0.4 C A:HIS181 4.3 12.9 1.0 O A:HOH990 4.4 28.2 1.0 CD1 A:PHE238 4.4 13.2 1.0 C4 A:5A0602 4.5 25.9 0.4 C4 A:5A0601 4.5 10.3 0.6 N A:ALA182 4.5 12.6 1.0 CA A:ALA182 4.6 12.4 1.0 CG A:LEU177 4.6 11.9 1.0 CA A:SER155 4.7 12.8 1.0 C2 A:DMS607 4.7 23.2 0.4 C5 A:5A0602 4.8 26.2 0.4 C5 A:5A0601 4.9 10.2 0.6 CB A:LEU177 4.9 11.5 1.0 O A:SER178 4.9 12.8 1.0 N A:HIS181 5.0 13.5 1.0 CA A:HIS181 5.0 13.4 1.0

Fluorine binding site 2 out of 4 in the Menin in Complex with Mi-859


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-859 within 5.0Å range: probe atom residue distance (Å) B Occ A:F601 b:15.8 occ:0.60 FAD A:5A0601 0.0 15.8 0.6 CAW A:5A0602 1.4 20.1 0.4 CAW A:5A0601 1.4 12.8 0.6 FAC A:5A0602 2.1 17.2 0.4 FAC A:5A0601 2.3 14.1 0.6 FAD A:5A0602 2.3 21.0 0.4 CAL A:5A0602 2.4 21.3 0.4 CAL A:5A0601 2.4 11.9 0.6 O A:HOH990 2.5 28.2 1.0 C A:HIS181 3.2 12.9 1.0 CA A:HIS181 3.2 13.4 1.0 N A:HIS181 3.3 13.5 1.0 O A:HIS181 3.4 12.6 1.0 O A:HOH970 3.6 28.9 1.0 N A:ALA182 3.6 12.6 1.0 CB A:SER155 3.6 12.6 1.0 C A:ASP180 3.7 14.3 1.0 CAS A:5A0602 3.7 23.3 0.4 CAS A:5A0601 3.7 10.9 0.6 O A:ASP180 4.0 15.0 1.0 CB A:ALA182 4.1 12.6 1.0 O A:HOH720 4.1 23.5 1.0 OG A:SER155 4.2 13.3 1.0 CA A:ALA182 4.4 12.4 1.0 CA A:ASP180 4.5 15.2 1.0 O A:HOH922 4.6 22.2 1.0 CAF A:5A0602 4.6 25.4 0.4 CAF A:5A0601 4.6 11.0 0.6 SAQ A:5A0602 4.6 25.6 0.4 SAQ A:5A0601 4.6 10.4 0.6 CA A:SER155 4.7 12.8 1.0 CB A:HIS181 4.8 13.7 1.0 O A:SER178 4.9 12.8 1.0 N A:ASP180 5.0 13.9 1.0

Fluorine binding site 3 out of 4 in the Menin in Complex with Mi-859


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-859 within 5.0Å range: probe atom residue distance (Å) B Occ A:F602 b:17.2 occ:0.40 FAC A:5A0602 0.0 17.2 0.4 CAW A:5A0601 1.3 12.8 0.6 CAW A:5A0602 1.4 20.1 0.4 FAD A:5A0601 2.1 15.8 0.6 FAD A:5A0602 2.3 21.0 0.4 FAC A:5A0601 2.3 14.1 0.6 CAL A:5A0601 2.4 11.9 0.6 CAL A:5A0602 2.4 21.3 0.4 CAS A:5A0602 2.9 23.3 0.4 CAS A:5A0601 2.9 10.9 0.6 C1 A:DMS608 3.1 21.9 0.4 CAF A:5A0602 3.3 25.4 0.4 O A:HOH990 3.3 28.2 1.0 CAF A:5A0601 3.3 11.0 0.6 S A:DMS607 3.4 23.1 0.4 OG A:SER155 3.5 13.3 1.0 O A:HOH970 3.5 28.9 1.0 CB A:SER155 3.6 12.6 1.0 C2 A:DMS607 3.8 23.2 0.4 O A:DMS607 3.8 22.9 0.4 SAQ A:5A0602 3.8 25.6 0.4 SAQ A:5A0601 3.8 10.4 0.6 O A:HOH922 4.1 22.2 1.0 C5 A:5A0602 4.3 26.2 0.4 C5 A:5A0601 4.3 10.2 0.6 S A:DMS608 4.6 23.7 0.4 C4 A:5A0602 4.6 25.9 0.4 C4 A:5A0601 4.6 10.3 0.6 O A:DMS608 4.7 20.8 0.4 CE1 A:PHE238 4.7 13.6 1.0 N A:HIS181 5.0 13.5 1.0 C1 A:DMS607 5.0 22.0 0.4

Fluorine binding site 4 out of 4 in the Menin in Complex with Mi-859


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-859 within 5.0Å range: probe atom residue distance (Å) B Occ A:F602 b:21.0 occ:0.40 FAD A:5A0602 0.0 21.0 0.4 FAC A:5A0601 0.1 14.1 0.6 CAW A:5A0602 1.4 20.1 0.4 CAW A:5A0601 1.4 12.8 0.6 FAC A:5A0602 2.3 17.2 0.4 FAD A:5A0601 2.3 15.8 0.6 CAL A:5A0602 2.4 21.3 0.4 CAL A:5A0601 2.4 11.9 0.6 CAS A:5A0602 2.8 23.3 0.4 CAS A:5A0601 2.9 10.9 0.6 SAQ A:5A0602 3.0 25.6 0.4 SAQ A:5A0601 3.0 10.4 0.6 CE1 A:PHE238 3.3 13.6 1.0 CB A:SER155 3.3 12.6 1.0 CD2 A:LEU177 3.4 12.1 1.0 OG A:SER155 3.8 13.3 1.0 C1 A:DMS608 3.8 21.9 0.4 CB A:ALA182 3.9 12.6 1.0 CAF A:5A0602 4.0 25.4 0.4 CZ A:PHE238 4.0 13.5 1.0 CAF A:5A0601 4.0 11.0 0.6 O A:HIS181 4.1 12.6 1.0 S A:DMS607 4.1 23.1 0.4 CD1 A:PHE238 4.3 13.2 1.0 C A:HIS181 4.4 12.9 1.0 C4 A:5A0602 4.4 25.9 0.4 C4 A:5A0601 4.4 10.3 0.6 O A:HOH990 4.4 28.2 1.0 CG A:LEU177 4.6 11.9 1.0 N A:ALA182 4.6 12.6 1.0 C2 A:DMS607 4.6 23.2 0.4 CA A:ALA182 4.7 12.4 1.0 CA A:SER155 4.7 12.8 1.0 C5 A:5A0602 4.8 26.2 0.4 C5 A:5A0601 4.8 10.2 0.6 CB A:LEU177 4.9 11.5 1.0 O A:SER178 5.0 12.8 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