Fluorine in PDB 6by8: Menin in Complex with Mi-1482

The structure of Menin in Complex with Mi-1482, PDB code: 6by8 was solved by T.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)	38.52 / 1.90
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	48.991, 80.222, 124.722, 90.00, 90.00, 90.00
R / Rfree (%)	15.1 / 18.8

The binding sites of Fluorine atom in the Menin in Complex with Mi-1482 (pdb code 6by8). 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-1482, PDB code: 6by8:
Jump to Fluorine binding site number: 1; 2; 3;

Fluorine binding site 1 out of 3 in the Menin in Complex with Mi-1482


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-1482 within 5.0Å range: probe atom residue distance (Å) B Occ A:F601 b:10.0 occ:1.00 FAD A:FNV601 0.0 10.0 1.0 CBP A:FNV601 1.3 12.1 1.0 FAE A:FNV601 2.1 8.8 1.0 FAF A:FNV601 2.1 10.3 1.0 CAT A:FNV601 2.4 5.2 1.0 CBD A:FNV601 2.9 5.4 1.0 O A:HOH1007 2.9 23.2 1.0 CAK A:FNV601 3.4 9.2 1.0 O A:HOH1029 3.5 43.3 1.0 OG A:SER155 3.6 9.2 1.0 O A:HOH959 3.6 20.2 1.0 S A:DMS602 3.7 21.8 0.9 CB A:SER155 3.7 7.7 1.0 C2 A:DMS602 3.9 19.6 0.9 SBA A:FNV601 3.9 8.7 1.0 O A:DMS602 4.0 26.7 0.9 O A:HOH857 4.1 16.1 1.0 C5 A:FNV601 4.4 9.7 1.0 CE1 A:PHE238 4.7 5.1 1.0 C4 A:FNV601 4.7 10.8 1.0 N A:HIS181 4.7 6.2 1.0 C A:ASP180 4.8 8.8 1.0

Fluorine binding site 2 out of 3 in the Menin in Complex with Mi-1482


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-1482 within 5.0Å range: probe atom residue distance (Å) B Occ A:F601 b:8.8 occ:1.00 FAE A:FNV601 0.0 8.8 1.0 CBP A:FNV601 1.3 12.1 1.0 FAF A:FNV601 2.1 10.3 1.0 FAD A:FNV601 2.1 10.0 1.0 CAT A:FNV601 2.3 5.2 1.0 C A:HIS181 3.0 6.0 1.0 N A:HIS181 3.1 6.2 1.0 CA A:HIS181 3.2 6.7 1.0 O A:HIS181 3.2 7.8 1.0 O A:HOH959 3.2 20.2 1.0 N A:ALA182 3.5 5.5 1.0 O A:HOH1007 3.5 23.2 1.0 CB A:SER155 3.6 7.7 1.0 CBD A:FNV601 3.6 5.4 1.0 C A:ASP180 3.7 8.8 1.0 O A:HOH742 3.8 24.7 1.0 CB A:ALA182 3.9 5.5 1.0 O A:ASP180 4.0 8.0 1.0 CA A:ALA182 4.2 5.5 1.0 OG A:SER155 4.3 9.2 1.0 CA A:ASP180 4.5 8.2 1.0 CAK A:FNV601 4.6 9.2 1.0 SBA A:FNV601 4.6 8.7 1.0 O A:HOH857 4.7 16.1 1.0 CB A:HIS181 4.7 5.8 1.0 CA A:SER155 4.8 7.8 1.0 O A:SER178 4.9 7.5 1.0 N A:ASP180 4.9 5.6 1.0

Fluorine binding site 3 out of 3 in the Menin in Complex with Mi-1482


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-1482 within 5.0Å range: probe atom residue distance (Å) B Occ A:F601 b:10.3 occ:1.00 FAF A:FNV601 0.0 10.3 1.0 CBP A:FNV601 1.3 12.1 1.0 FAE A:FNV601 2.1 8.8 1.0 FAD A:FNV601 2.1 10.0 1.0 CAT A:FNV601 2.4 5.2 1.0 CBD A:FNV601 2.9 5.4 1.0 SBA A:FNV601 3.2 8.7 1.0 CB A:SER155 3.3 7.7 1.0 CE1 A:PHE238 3.4 5.1 1.0 CD2 A:LEU177 3.6 5.9 1.0 OG A:SER155 3.8 9.2 1.0 CB A:ALA182 3.9 5.5 1.0 CZ A:PHE238 4.0 9.5 1.0 O A:HIS181 4.0 7.8 1.0 CAK A:FNV601 4.0 9.2 1.0 C A:HIS181 4.3 6.0 1.0 S A:DMS602 4.3 21.8 0.9 CD1 A:PHE238 4.5 5.8 1.0 C4 A:FNV601 4.5 10.8 1.0 C2 A:DMS602 4.6 19.6 0.9 N A:ALA182 4.6 5.5 1.0 CA A:ALA182 4.7 5.5 1.0 CG A:LEU177 4.7 7.8 1.0 CA A:SER155 4.8 7.8 1.0 O A:HOH1007 4.8 23.2 1.0 C5 A:FNV601 4.8 9.7 1.0 N A:HIS181 4.8 6.2 1.0 O A:HOH959 4.9 20.2 1.0 CA A:HIS181 4.9 6.7 1.0 O A:SER178 5.0 7.5 1.0 CB A:LEU177 5.0 7.2 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