Fluorine in PDB 5ddb: Menin in Complex with Mi-319

The structure of Menin in Complex with Mi-319, PDB code: 5ddb 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)	41.46 / 1.54
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	48.413, 80.054, 124.728, 90.00, 90.00, 90.00
R / Rfree (%)	17.2 / 21

The binding sites of Fluorine atom in the Menin in Complex with Mi-319 (pdb code 5ddb). 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-319, PDB code: 5ddb:
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-319


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-319 within 5.0Å range: probe atom residue distance (Å) B Occ A:F601 b:18.4 occ:0.90 FAC A:59Q601 0.0 18.4 0.9 CBB A:59Q601 1.3 20.4 0.9 FAE A:59Q601 2.0 20.5 0.9 FAD A:59Q601 2.1 19.6 0.9 CAL A:59Q601 2.4 18.2 0.9 O A:HOH982 3.0 36.5 1.0 C A:HIS181 3.1 14.1 1.0 CA A:HIS181 3.2 12.5 1.0 N A:HIS181 3.2 11.9 1.0 O A:HIS181 3.4 13.7 1.0 O A:HOH990 3.5 34.0 1.0 C A:ASP180 3.6 13.2 1.0 N A:ALA182 3.6 12.4 1.0 CAS A:59Q601 3.7 16.7 0.9 CB A:SER155 3.7 16.7 1.0 O A:ASP180 3.9 16.1 1.0 O A:HOH718 4.0 28.5 1.0 CB A:ALA182 4.0 12.9 1.0 OG A:SER155 4.3 16.1 1.0 CA A:ALA182 4.4 11.8 1.0 CA A:ASP180 4.4 14.2 1.0 O A:HOH783 4.5 23.9 1.0 CAG A:59Q601 4.6 16.5 0.9 SAR A:59Q601 4.6 16.7 0.9 CB A:HIS181 4.7 13.2 1.0 CA A:SER155 4.8 12.9 1.0 N A:ASP180 4.9 12.8 1.0

Fluorine binding site 2 out of 5 in the Menin in Complex with Mi-319


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-319 within 5.0Å range: probe atom residue distance (Å) B Occ A:F601 b:19.6 occ:0.90 FAD A:59Q601 0.0 19.6 0.9 CBB A:59Q601 1.3 20.4 0.9 FAE A:59Q601 2.0 20.5 0.9 FAC A:59Q601 2.1 18.4 0.9 CAL A:59Q601 2.3 18.2 0.9 CAS A:59Q601 2.9 16.7 0.9 SAR A:59Q601 3.2 16.7 0.9 CB A:SER155 3.2 16.7 1.0 CD2 A:LEU177 3.6 15.4 1.0 CE1 A:PHE238 3.7 15.1 1.0 OG A:SER155 3.7 16.1 1.0 CB A:ALA182 3.8 12.9 1.0 O A:HIS181 3.9 13.7 1.0 CAG A:59Q601 4.0 16.5 0.9 C A:HIS181 4.1 14.1 1.0 CZ A:PHE238 4.2 16.4 1.0 C1 A:DMS607 4.4 35.9 0.5 S A:DMS602 4.4 23.4 0.5 N A:ALA182 4.4 12.4 1.0 C4 A:59Q601 4.5 19.2 0.9 CA A:ALA182 4.6 11.8 1.0 CA A:SER155 4.7 12.9 1.0 N A:HIS181 4.7 11.9 1.0 O A:HOH982 4.7 36.5 1.0 CA A:HIS181 4.8 12.5 1.0 CD1 A:PHE238 4.8 15.8 1.0 C5 A:59Q601 4.8 18.6 0.9 CG A:LEU177 4.8 15.3 1.0 O A:HOH990 4.9 34.0 1.0 C2 A:DMS602 4.9 22.9 0.5 O A:SER178 5.0 14.4 1.0

Fluorine binding site 3 out of 5 in the Menin in Complex with Mi-319


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-319 within 5.0Å range: probe atom residue distance (Å) B Occ A:F601 b:20.5 occ:0.90 FAE A:59Q601 0.0 20.5 0.9 CBB A:59Q601 1.2 20.4 0.9 FAD A:59Q601 2.0 19.6 0.9 FAC A:59Q601 2.0 18.4 0.9 CAL A:59Q601 2.3 18.2 0.9 CAS A:59Q601 2.8 16.7 0.9 O A:HOH990 3.2 34.0 1.0 CAG A:59Q601 3.4 16.5 0.9 OG A:SER155 3.5 16.1 1.0 CB A:SER155 3.6 16.7 1.0 O A:HOH982 3.7 36.5 1.0 C1 A:DMS607 3.7 35.9 0.5 S A:DMS602 3.7 23.4 0.5 O A:DMS602 3.8 25.2 0.5 SAR A:59Q601 3.9 16.7 0.9 O A:HOH783 4.0 23.9 1.0 C2 A:DMS602 4.2 22.9 0.5 C5 A:59Q601 4.4 18.6 0.9 C4 A:59Q601 4.6 19.2 0.9 CE1 A:PHE238 4.8 15.1 1.0 N A:HIS181 4.8 11.9 1.0 O A:DMS607 4.8 31.4 0.5 C A:ASP180 4.9 13.2 1.0 S A:DMS607 4.9 37.0 0.5 CA A:SER155 5.0 12.9 1.0

Fluorine binding site 4 out of 5 in the Menin in Complex with Mi-319


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-319 within 5.0Å range: probe atom residue distance (Å) B Occ A:F601 b:42.5 occ:0.90 FAA A:59Q601 0.0 42.5 0.9 CAY A:59Q601 1.4 30.5 0.9 FAB A:59Q601 2.3 30.0 0.9 CAT A:59Q601 2.4 20.6 0.9 SAQ A:59Q601 3.3 20.9 0.9 NAO A:59Q601 3.4 24.4 0.9 CB A:MET322 3.6 17.7 0.5 CB A:MET322 3.6 15.8 0.5 OE2 A:GLU363 4.1 54.9 1.0 CD1 A:TYR319 4.1 17.7 1.0 C A:MET322 4.3 14.2 1.0 O A:HOH1050 4.3 49.4 1.0 O A:HOH998 4.3 38.3 1.0 O A:MET322 4.3 15.1 1.0 CE1 A:TYR319 4.4 20.6 1.0 NAP A:59Q601 4.4 25.7 0.9 SD A:MET322 4.4 22.0 0.5 CG A:MET322 4.5 32.8 0.5 CAU A:59Q601 4.5 22.3 0.9 N A:TYR323 4.5 14.0 1.0 CA A:MET322 4.6 13.9 0.5 CA A:MET322 4.6 13.3 0.5 O A:HOH888 4.6 31.4 1.0 CG A:MET322 4.7 25.5 0.5 O A:HOH761 4.8 27.1 1.0 SD A:MET322 4.9 16.3 0.5 CA A:TYR323 5.0 14.6 1.0 CD A:GLU363 5.0 40.5 0.6 CG A:TYR319 5.0 15.2 1.0

Fluorine binding site 5 out of 5 in the Menin in Complex with Mi-319


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-319 within 5.0Å range: probe atom residue distance (Å) B Occ A:F601 b:30.0 occ:0.90 FAB A:59Q601 0.0 30.0 0.9 CAY A:59Q601 1.4 30.5 0.9 FAA A:59Q601 2.3 42.5 0.9 CAT A:59Q601 2.4 20.6 0.9 N A:TYR323 2.8 14.0 1.0 SAQ A:59Q601 3.1 20.9 0.9 CB A:MET322 3.1 17.7 0.5 C A:MET322 3.2 14.2 1.0 CB A:MET322 3.3 15.8 0.5 CA A:TYR323 3.3 14.6 1.0 CG A:TYR323 3.4 15.7 1.0 O A:TYR319 3.4 15.4 1.0 CD2 A:TYR323 3.5 17.1 1.0 NAO A:59Q601 3.5 24.4 0.9 CA A:MET322 3.7 13.9 0.5 CA A:MET322 3.8 13.3 0.5 O A:MET322 3.8 15.1 1.0 CB A:TYR323 3.8 14.3 1.0 CD1 A:TYR323 3.8 17.6 1.0 CD1 A:TYR319 3.9 17.7 1.0 CE2 A:TYR323 3.9 16.3 1.0 CB A:TYR319 4.0 13.6 1.0 CA A:TYR319 4.1 13.3 1.0 CG A:TYR319 4.2 15.2 1.0 C A:TYR319 4.2 13.2 1.0 CE1 A:TYR323 4.3 19.1 1.0 CZ A:TYR323 4.3 18.9 1.0 CAU A:59Q601 4.4 22.3 0.9 CG A:MET322 4.5 32.8 0.5 N A:MET322 4.5 14.7 1.0 NAP A:59Q601 4.5 25.7 0.9 CG A:MET322 4.6 25.5 0.5 C A:TYR323 4.7 15.6 1.0 O A:HOH998 4.8 38.3 1.0 CE1 A:TYR319 4.8 20.6 1.0 O A:HOH761 4.9 27.1 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