Fluorine in PDB 5db3: Menin in Complex with Mi-574

The structure of Menin in Complex with Mi-574, PDB code: 5db3 was solved by J.Pollock, D.Borkin, T.Cierpicki, J.Grembecka, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	41.82 / 1.71
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	48.899, 80.456, 125.093, 90.00, 90.00, 90.00
R / Rfree (%)	16.1 / 19.4

The binding sites of Fluorine atom in the Menin in Complex with Mi-574 (pdb code 5db3). 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-574, PDB code: 5db3:
Jump to Fluorine binding site number: 1; 2; 3;

Fluorine binding site 1 out of 3 in the Menin in Complex with Mi-574


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-574 within 5.0Å range: probe atom residue distance (Å) B Occ A:F610 b:9.8 occ:1.00 FAD A:58Q610 0.0 9.8 1.0 CBP A:58Q610 1.3 10.8 1.0 FAF A:58Q610 2.1 12.7 1.0 FAE A:58Q610 2.1 12.0 1.0 CAT A:58Q610 2.3 9.8 1.0 C A:HIS181 3.0 8.8 1.0 CA A:HIS181 3.1 9.2 1.0 N A:HIS181 3.1 9.9 1.0 O A:HIS181 3.2 8.6 1.0 O A:HOH1033 3.3 20.8 1.0 N A:ALA182 3.5 9.0 1.0 O A:HOH953 3.6 26.9 1.0 CB A:SER155 3.6 11.1 1.0 C A:ASP180 3.7 9.9 1.0 CBE A:58Q610 3.7 9.9 1.0 O A:HOH713 3.9 25.3 1.0 CB A:ALA182 4.0 9.6 1.0 O A:ASP180 4.1 11.1 1.0 OG A:SER155 4.2 11.4 1.0 CA A:ALA182 4.2 9.1 1.0 CA A:ASP180 4.5 10.2 1.0 O A:HOH749 4.5 20.5 1.0 CAL A:58Q610 4.6 10.2 1.0 CB A:HIS181 4.6 10.1 1.0 SBA A:58Q610 4.7 9.6 1.0 CA A:SER155 4.8 10.8 1.0 CD2 A:LEU177 4.9 9.5 1.0 O A:SER178 4.9 9.7 1.0 N A:ASP180 4.9 8.7 1.0

Fluorine binding site 2 out of 3 in the Menin in Complex with Mi-574


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-574 within 5.0Å range: probe atom residue distance (Å) B Occ A:F610 b:12.0 occ:1.00 FAE A:58Q610 0.0 12.0 1.0 CBP A:58Q610 1.4 10.8 1.0 FAF A:58Q610 2.1 12.7 1.0 FAD A:58Q610 2.1 9.8 1.0 CAT A:58Q610 2.4 9.8 1.0 CBE A:58Q610 2.9 9.9 1.0 SBA A:58Q610 3.2 9.6 1.0 CB A:SER155 3.3 11.1 1.0 CE1 A:PHE238 3.5 9.7 1.0 CD2 A:LEU177 3.5 9.5 1.0 OG A:SER155 3.7 11.4 1.0 CB A:ALA182 4.0 9.6 1.0 CAL A:58Q610 4.0 10.2 1.0 CZ A:PHE238 4.0 10.7 1.0 O A:HIS181 4.0 8.6 1.0 S A:DMS601 4.2 26.3 1.0 C A:HIS181 4.3 8.8 1.0 C2 A:DMS601 4.5 26.7 1.0 CD1 A:PHE238 4.5 9.5 1.0 C4 A:58Q610 4.5 10.8 1.0 N A:ALA182 4.6 9.0 1.0 CA A:SER155 4.7 10.8 1.0 CA A:ALA182 4.7 9.1 1.0 C5 A:58Q610 4.8 9.4 1.0 CG A:LEU177 4.8 9.2 1.0 N A:HIS181 4.9 9.9 1.0 CA A:HIS181 5.0 9.2 1.0 O A:HOH1033 5.0 20.8 1.0 O A:HOH953 5.0 26.9 1.0

Fluorine binding site 3 out of 3 in the Menin in Complex with Mi-574


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-574 within 5.0Å range: probe atom residue distance (Å) B Occ A:F610 b:12.7 occ:1.00 FAF A:58Q610 0.0 12.7 1.0 CBP A:58Q610 1.3 10.8 1.0 FAE A:58Q610 2.1 12.0 1.0 FAD A:58Q610 2.1 9.8 1.0 CAT A:58Q610 2.4 9.8 1.0 CBE A:58Q610 2.9 9.9 1.0 O A:HOH953 3.1 26.9 1.0 CAL A:58Q610 3.4 10.2 1.0 OG A:SER155 3.6 11.4 1.0 O A:HOH994 3.6 40.5 1.0 S A:DMS601 3.7 26.3 1.0 CB A:SER155 3.7 11.1 1.0 O A:HOH1033 3.8 20.8 1.0 O A:HOH749 3.9 20.5 1.0 C2 A:DMS601 4.0 26.7 1.0 SBA A:58Q610 4.0 9.6 1.0 O A:DMS601 4.1 29.6 1.0 C5 A:58Q610 4.4 9.4 1.0 N A:HIS181 4.7 9.9 1.0 C4 A:58Q610 4.7 10.8 1.0 C A:ASP180 4.8 9.9 1.0 CE1 A:PHE238 4.9 9.7 1.0 O A:HOH1046 4.9 42.1 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