Fluorine in PDB 6bxy: Menin in Complex with Mi-1481

The structure of Menin in Complex with Mi-1481, PDB code: 6bxy was solved by D.Borkin, S.Klossowski, J.Pollock, B.Linhares, T.Cierpicki, J.Grembecka, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	40.27 / 1.82
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	47.319, 80.539, 122.341, 90.00, 90.00, 90.00
R / Rfree (%)	17.4 / 21.3

The binding sites of Fluorine atom in the Menin in Complex with Mi-1481 (pdb code 6bxy). 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-1481, PDB code: 6bxy:
Jump to Fluorine binding site number: 1; 2; 3;

Fluorine binding site 1 out of 3 in the Menin in Complex with Mi-1481


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-1481 within 5.0Å range: probe atom residue distance (Å) B Occ A:F601 b:15.5 occ:1.00 FAD A:EEV601 0.0 15.5 1.0 CBP A:EEV601 1.2 15.4 1.0 FAE A:EEV601 2.0 15.9 1.0 FAF A:EEV601 2.1 12.7 1.0 CAT A:EEV601 2.4 10.8 1.0 CBD A:EEV601 2.9 12.3 1.0 CB A:SER155 3.2 12.0 1.0 SBA A:EEV601 3.3 14.1 1.0 CE1 A:PHE238 3.5 15.9 1.0 CD2 A:LEU177 3.6 9.9 1.0 OG A:SER155 3.7 13.1 1.0 CB A:ALA182 4.0 12.5 1.0 CZ A:PHE238 4.0 17.3 1.0 CAK A:EEV601 4.0 12.8 1.0 O A:HIS181 4.1 12.6 1.0 S A:DMS602 4.2 30.1 0.8 C A:HIS181 4.4 9.6 1.0 CD1 A:PHE238 4.5 14.1 1.0 C2 A:DMS602 4.6 28.0 0.8 C4 A:EEV601 4.6 13.0 1.0 N A:ALA182 4.6 9.8 1.0 CA A:SER155 4.7 9.5 1.0 CA A:ALA182 4.8 11.3 1.0 O A:HOH783 4.8 26.1 1.0 C5 A:EEV601 4.8 13.7 1.0 O A:HOH840 4.8 31.6 1.0 N A:HIS181 4.9 9.8 1.0 CG A:LEU177 4.9 10.3 1.0 O A:SER178 5.0 12.4 1.0

Fluorine binding site 2 out of 3 in the Menin in Complex with Mi-1481


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-1481 within 5.0Å range: probe atom residue distance (Å) B Occ A:F601 b:15.9 occ:1.00 FAE A:EEV601 0.0 15.9 1.0 CBP A:EEV601 1.3 15.4 1.0 FAD A:EEV601 2.0 15.5 1.0 FAF A:EEV601 2.2 12.7 1.0 CAT A:EEV601 2.5 10.8 1.0 CBD A:EEV601 2.9 12.3 1.0 O A:HOH783 3.1 26.1 1.0 CAK A:EEV601 3.4 12.8 1.0 OG A:SER155 3.5 13.1 1.0 S A:DMS602 3.5 30.1 0.8 CB A:SER155 3.6 12.0 1.0 O A:HOH840 3.8 31.6 1.0 O A:DMS602 3.9 33.5 0.8 SBA A:EEV601 3.9 14.1 1.0 C2 A:DMS602 4.0 28.0 0.8 O A:HOH756 4.1 23.4 1.0 C5 A:EEV601 4.4 13.7 1.0 CE1 A:PHE238 4.7 15.9 1.0 C4 A:EEV601 4.7 13.0 1.0 N A:HIS181 4.8 9.8 1.0 C A:ASP180 4.9 13.2 1.0

Fluorine binding site 3 out of 3 in the Menin in Complex with Mi-1481


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-1481 within 5.0Å range: probe atom residue distance (Å) B Occ A:F601 b:12.7 occ:1.00 FAF A:EEV601 0.0 12.7 1.0 CBP A:EEV601 1.4 15.4 1.0 FAD A:EEV601 2.1 15.5 1.0 FAE A:EEV601 2.2 15.9 1.0 CAT A:EEV601 2.5 10.8 1.0 C A:HIS181 2.9 9.6 1.0 N A:HIS181 3.1 9.8 1.0 CA A:HIS181 3.1 10.2 1.0 O A:HIS181 3.2 12.6 1.0 O A:HOH840 3.2 31.6 1.0 N A:ALA182 3.4 9.8 1.0 O A:HOH730 3.6 30.6 1.0 CB A:SER155 3.6 12.0 1.0 C A:ASP180 3.7 13.2 1.0 O A:HOH783 3.7 26.1 1.0 CBD A:EEV601 3.8 12.3 1.0 CB A:ALA182 3.9 12.5 1.0 O A:ASP180 4.0 12.4 1.0 CA A:ALA182 4.2 11.3 1.0 OG A:SER155 4.3 13.1 1.0 CA A:ASP180 4.5 11.6 1.0 CA A:SER155 4.7 9.5 1.0 CB A:HIS181 4.7 13.0 1.0 O A:HOH756 4.7 23.4 1.0 CAK A:EEV601 4.7 12.8 1.0 SBA A:EEV601 4.8 14.1 1.0 O A:SER178 4.9 12.4 1.0 N A:ASP180 5.0 10.3 1.0 CD2 A:LEU177 5.0 9.9 1.0

D.Borkin, S.Klossowski, J.Pollock, H.Miao, B.M.Linhares, K.Kempinska, Z.Jin, T.Purohit, B.Wen, M.He, D.Sun, T.Cierpicki, J.Grembecka. Complexity of Blocking Bivalent Protein-Protein Interactions: Development of A Highly Potent Inhibitor of the Menin-Mixed-Lineage Leukemia Interaction. J.Med.Chem. V. 61 4832 2018.
ISSN: ISSN 0022-2623
PubMed: 29738674
DOI: 10.1021/ACS.JMEDCHEM.8B00071