Fluorine in PDB 5db2: Menin in Complex with Mi-389

The structure of Menin in Complex with Mi-389, PDB code: 5db2 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)	38.10 / 1.54
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	49.086, 79.976, 124.428, 90.00, 90.00, 90.00
R / Rfree (%)	15.9 / 18.8

The binding sites of Fluorine atom in the Menin in Complex with Mi-389 (pdb code 5db2). 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-389, PDB code: 5db2:
Jump to Fluorine binding site number: 1; 2; 3;

Fluorine binding site 1 out of 3 in the Menin in Complex with Mi-389


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-389 within 5.0Å range: probe atom residue distance (Å) B Occ A:F601 b:8.5 occ:1.00 FAD A:58R601 0.0 8.5 1.0 CBK A:58R601 1.3 8.6 1.0 FAF A:58R601 2.1 10.5 1.0 FAE A:58R601 2.2 9.4 1.0 CAT A:58R601 2.3 7.8 1.0 C A:HIS181 3.0 6.4 1.0 CA A:HIS181 3.1 6.7 1.0 N A:HIS181 3.2 7.0 1.0 O A:HIS181 3.2 7.1 1.0 O A:HOH1100 3.2 20.9 1.0 N A:ALA182 3.5 6.1 1.0 CBA A:58R601 3.6 6.9 1.0 C A:ASP180 3.6 7.9 1.0 CB A:SER155 3.7 8.9 1.0 O A:HOH1051 3.7 22.4 1.0 CB A:ALA182 3.9 6.7 1.0 O A:HOH724 3.9 23.4 1.0 O A:ASP180 4.0 8.7 1.0 OG A:SER155 4.2 9.7 1.0 CA A:ALA182 4.2 6.0 1.0 CA A:ASP180 4.5 8.0 1.0 CAM A:58R601 4.6 7.1 1.0 O A:HOH802 4.6 17.4 1.0 CB A:HIS181 4.7 7.3 1.0 SAX A:58R601 4.7 7.7 1.0 CA A:SER155 4.8 8.1 1.0 O A:SER178 4.9 6.5 1.0 N A:ASP180 4.9 7.1 1.0 CD2 A:LEU177 5.0 7.7 1.0

Fluorine binding site 2 out of 3 in the Menin in Complex with Mi-389


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-389 within 5.0Å range: probe atom residue distance (Å) B Occ A:F601 b:9.4 occ:1.00 FAE A:58R601 0.0 9.4 1.0 CBK A:58R601 1.3 8.6 1.0 FAF A:58R601 2.1 10.5 1.0 FAD A:58R601 2.2 8.5 1.0 CAT A:58R601 2.4 7.8 1.0 CBA A:58R601 2.9 6.9 1.0 SAX A:58R601 3.2 7.7 1.0 CB A:SER155 3.3 8.9 1.0 CE1 A:PHE238 3.5 7.1 1.0 CD2 A:LEU177 3.5 7.7 1.0 OG A:SER155 3.7 9.7 1.0 CB A:ALA182 3.8 6.7 1.0 CZ A:PHE238 4.0 7.9 1.0 CAM A:58R601 4.0 7.1 1.0 O A:HIS181 4.0 7.1 1.0 S A:DMS602 4.2 18.1 1.0 C A:HIS181 4.3 6.4 1.0 CD1 A:PHE238 4.5 6.9 1.0 C4 A:58R601 4.5 7.0 1.0 C2 A:DMS602 4.6 18.5 1.0 N A:ALA182 4.6 6.1 1.0 CA A:ALA182 4.7 6.0 1.0 CG A:LEU177 4.7 7.2 1.0 CA A:SER155 4.7 8.1 1.0 C5 A:58R601 4.8 6.7 1.0 N A:HIS181 4.9 7.0 1.0 O A:HOH1051 4.9 22.4 1.0 CA A:HIS181 5.0 6.7 1.0 O A:SER178 5.0 6.5 1.0 O A:HOH1100 5.0 20.9 1.0

Fluorine binding site 3 out of 3 in the Menin in Complex with Mi-389


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-389 within 5.0Å range: probe atom residue distance (Å) B Occ A:F601 b:10.5 occ:1.00 FAF A:58R601 0.0 10.5 1.0 CBK A:58R601 1.3 8.6 1.0 FAE A:58R601 2.1 9.4 1.0 FAD A:58R601 2.1 8.5 1.0 CAT A:58R601 2.4 7.8 1.0 CBA A:58R601 2.8 6.9 1.0 O A:HOH1051 3.1 22.4 1.0 CAM A:58R601 3.3 7.1 1.0 OG A:SER155 3.5 9.7 1.0 S A:DMS602 3.6 18.1 1.0 O A:HOH942 3.6 30.7 1.0 O A:HOH1100 3.7 20.9 1.0 CB A:SER155 3.7 8.9 1.0 SAX A:58R601 3.9 7.7 1.0 C2 A:DMS602 4.0 18.5 1.0 O A:HOH802 4.0 17.4 1.0 O A:DMS602 4.0 21.1 1.0 C5 A:58R601 4.4 6.7 1.0 C4 A:58R601 4.6 7.0 1.0 CE1 A:PHE238 4.7 7.1 1.0 N A:HIS181 4.8 7.0 1.0 C A:ASP180 4.9 7.9 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