Fluorine in PDB 5db1: Menin in Complex with Mi-336

The structure of Menin in Complex with Mi-336, PDB code: 5db1 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)	39.94 / 1.86
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	48.318, 79.816, 124.780, 90.00, 90.00, 90.00
R / Rfree (%)	16.3 / 19.7

The binding sites of Fluorine atom in the Menin in Complex with Mi-336 (pdb code 5db1). 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-336, PDB code: 5db1:
Jump to Fluorine binding site number: 1; 2; 3;

Fluorine binding site 1 out of 3 in the Menin in Complex with Mi-336


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-336 within 5.0Å range: probe atom residue distance (Å) B Occ A:F601 b:14.9 occ:1.00 FAC A:58O601 0.0 14.9 1.0 CBI A:58O601 1.3 14.5 1.0 FAE A:58O601 2.1 15.6 1.0 FAD A:58O601 2.1 14.7 1.0 CAQ A:58O601 2.3 13.3 1.0 C A:HIS181 3.0 12.7 1.0 O A:HIS181 3.1 11.4 1.0 CA A:HIS181 3.2 12.4 1.0 N A:HIS181 3.2 12.6 1.0 O A:HOH982 3.3 25.8 1.0 N A:ALA182 3.5 12.3 1.0 CAY A:58O601 3.6 12.0 1.0 O A:HOH867 3.6 31.5 1.0 CB A:SER155 3.6 13.1 1.0 C A:ASP180 3.8 12.8 1.0 CB A:ALA182 3.9 12.5 1.0 O A:HOH708 3.9 27.6 1.0 CA A:ALA182 4.2 12.0 1.0 O A:ASP180 4.3 13.3 1.0 OG A:SER155 4.3 13.2 1.0 CA A:ASP180 4.5 13.5 1.0 CAJ A:58O601 4.6 12.9 1.0 O A:HOH844 4.6 21.7 1.0 SAW A:58O601 4.6 12.7 1.0 CB A:HIS181 4.7 13.5 1.0 CA A:SER155 4.8 12.4 1.0 N A:ASP180 5.0 12.6 1.0 O A:SER178 5.0 12.7 1.0

Fluorine binding site 2 out of 3 in the Menin in Complex with Mi-336


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-336 within 5.0Å range: probe atom residue distance (Å) B Occ A:F601 b:14.7 occ:1.00 FAD A:58O601 0.0 14.7 1.0 CBI A:58O601 1.3 14.5 1.0 FAE A:58O601 2.1 15.6 1.0 FAC A:58O601 2.1 14.9 1.0 CAQ A:58O601 2.4 13.3 1.0 CAY A:58O601 2.9 12.0 1.0 SAW A:58O601 3.2 12.7 1.0 CB A:SER155 3.3 13.1 1.0 CE1 A:PHE238 3.5 12.1 1.0 CD2 A:LEU177 3.6 12.3 1.0 OG A:SER155 3.7 13.2 1.0 CB A:ALA182 3.8 12.5 1.0 O A:HIS181 3.9 11.4 1.0 CZ A:PHE238 4.0 12.7 1.0 CAJ A:58O601 4.0 12.9 1.0 C A:HIS181 4.3 12.7 1.0 S A:DMS602 4.3 31.8 1.0 CD1 A:PHE238 4.5 13.2 1.0 C4 A:58O601 4.6 13.3 1.0 C2 A:DMS602 4.6 30.6 1.0 N A:ALA182 4.6 12.3 1.0 CA A:ALA182 4.7 12.0 1.0 CA A:SER155 4.7 12.4 1.0 CG A:LEU177 4.8 12.8 1.0 C5 A:58O601 4.8 12.8 1.0 N A:HIS181 4.9 12.6 1.0 CA A:HIS181 5.0 12.4 1.0 O A:HOH867 5.0 31.5 1.0

Fluorine binding site 3 out of 3 in the Menin in Complex with Mi-336


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-336 within 5.0Å range: probe atom residue distance (Å) B Occ A:F601 b:15.6 occ:1.00 FAE A:58O601 0.0 15.6 1.0 CBI A:58O601 1.3 14.5 1.0 FAC A:58O601 2.1 14.9 1.0 FAD A:58O601 2.1 14.7 1.0 CAQ A:58O601 2.3 13.3 1.0 CAY A:58O601 2.8 12.0 1.0 O A:HOH867 3.1 31.5 1.0 CAJ A:58O601 3.3 12.9 1.0 O A:HOH937 3.5 40.7 1.0 OG A:SER155 3.6 13.2 1.0 S A:DMS602 3.7 31.8 1.0 CB A:SER155 3.7 13.1 1.0 O A:HOH982 3.9 25.8 1.0 SAW A:58O601 3.9 12.7 1.0 C2 A:DMS602 3.9 30.6 1.0 O A:HOH844 4.0 21.7 1.0 O A:DMS602 4.0 37.6 1.0 C5 A:58O601 4.4 12.8 1.0 C4 A:58O601 4.7 13.3 1.0 N A:HIS181 4.7 12.6 1.0 CE1 A:PHE238 4.8 12.1 1.0 O A:HIS181 4.9 11.4 1.0 C A:ASP180 5.0 12.8 1.0

D.Borkin, J.Pollock, K.Kempinska, T.Purohit, X.Li, B.Wen, T.Zhao, H.Miao, S.Shukla, M.He, D.Sun, T.Cierpicki, J.Grembecka. Property Focused Structure-Based Optimization of Small Molecule Inhibitors of the Protein-Protein Interaction Between Menin and Mixed Lineage Leukemia (Mll). J.Med.Chem. V. 59 892 2016.
ISSN: ISSN 0022-2623
PubMed: 26744767
DOI: 10.1021/ACS.JMEDCHEM.5B01305