Fluorine in PDB 7kid: PRMT5:MEP50 Complexed with 5,5-Bicyclic Inhibitor Compound 72

All present enzymatic activity of PRMT5:MEP50 Complexed with 5,5-Bicyclic Inhibitor Compound 72:
2.1.1.320;

The structure of PRMT5:MEP50 Complexed with 5,5-Bicyclic Inhibitor Compound 72, PDB code: 7kid was solved by R.L.Palte, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	34.79 / 2.50
Space group	I 2 2 2
Cell size a, b, c (Å), α, β, γ (°)	103.678, 139.177, 178.883, 90, 90, 90
R / Rfree (%)	25.9 / 27.9

The binding sites of Fluorine atom in the PRMT5:MEP50 Complexed with 5,5-Bicyclic Inhibitor Compound 72 (pdb code 7kid). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 3 binding sites of Fluorine where determined in the PRMT5:MEP50 Complexed with 5,5-Bicyclic Inhibitor Compound 72, PDB code: 7kid:
Jump to Fluorine binding site number: 1; 2; 3;

Fluorine binding site 1 out of 3 in the PRMT5:MEP50 Complexed with 5,5-Bicyclic Inhibitor Compound 72


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of PRMT5:MEP50 Complexed with 5,5-Bicyclic Inhibitor Compound 72 within 5.0Å range: probe atom residue distance (Å) B Occ A:F705 b:32.6 occ:1.00 F2 A:WFV705 0.0 32.6 1.0 C17 A:WFV705 1.4 32.5 1.0 C16 A:WFV705 2.3 32.6 1.0 C18 A:WFV705 2.4 32.7 1.0 NZ A:LYS333 2.8 77.8 1.0 C23 A:WFV705 2.8 33.3 1.0 OE1 A:GLU435 2.9 50.9 1.0 CB A:PHE327 3.3 37.5 1.0 CG A:PHE327 3.3 38.8 1.0 OH A:TYR334 3.3 52.5 1.0 CD2 A:PHE327 3.5 40.7 1.0 C15 A:WFV705 3.6 32.8 1.0 C19 A:WFV705 3.6 32.6 1.0 CD A:GLU435 3.8 55.2 1.0 CD1 A:PHE327 3.9 41.6 1.0 CE A:LYS333 4.0 70.8 1.0 C20 A:WFV705 4.1 32.6 1.0 C22 A:WFV705 4.2 33.7 1.0 CA A:PHE327 4.2 35.9 1.0 O A:HOH802 4.2 9.9 0.7 CE2 A:PHE327 4.3 43.4 1.0 O A:PHE327 4.5 40.3 1.0 CZ A:TYR334 4.5 51.4 1.0 OE2 A:GLU435 4.6 48.0 1.0 CG A:GLU435 4.6 38.3 1.0 C A:PHE327 4.6 40.6 1.0 CE1 A:PHE327 4.6 42.4 1.0 CD A:LYS333 4.7 62.6 1.0 N4 A:WFV705 4.8 33.0 1.0 CZ A:PHE327 4.8 41.3 1.0 C14 A:WFV705 4.9 32.6 1.0 C21 A:WFV705 5.0 33.6 1.0

Fluorine binding site 2 out of 3 in the PRMT5:MEP50 Complexed with 5,5-Bicyclic Inhibitor Compound 72


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of PRMT5:MEP50 Complexed with 5,5-Bicyclic Inhibitor Compound 72 within 5.0Å range: probe atom residue distance (Å) B Occ A:F705 b:34.0 occ:1.00 F1 A:WFV705 0.0 34.0 1.0 C22 A:WFV705 1.4 33.7 1.0 C23 A:WFV705 2.3 33.3 1.0 C21 A:WFV705 2.4 33.6 1.0 O A:SER578 2.7 35.5 1.0 N5 A:WFV705 2.8 33.8 1.0 CD1 A:TRP579 3.3 32.8 1.0 C A:SER578 3.3 36.1 1.0 O A:HOH898 3.4 36.5 1.0 NE1 A:TRP579 3.4 32.3 1.0 C18 A:WFV705 3.6 32.7 1.0 O A:HOH913 3.6 34.7 1.0 N4 A:WFV705 3.6 33.0 1.0 CG A:TRP579 3.7 29.9 1.0 CB A:SER578 3.8 37.6 1.0 CE2 A:TRP579 4.0 33.7 1.0 N A:TRP579 4.0 31.1 1.0 CA A:SER578 4.1 34.2 1.0 C19 A:WFV705 4.1 32.6 1.0 CE1 A:PHE327 4.1 42.4 1.0 CD2 A:TRP579 4.2 29.8 1.0 CA A:TRP579 4.2 30.1 1.0 O A:HOH1014 4.3 53.0 1.0 CD1 A:PHE327 4.3 41.6 1.0 CB A:TRP579 4.5 28.9 1.0 O A:HOH957 4.6 21.8 1.0 OG A:SER578 4.6 46.2 1.0 C17 A:WFV705 4.8 32.5 1.0 CZ2 A:TRP579 4.9 33.1 1.0 CZ A:PHE327 4.9 41.3 1.0

Fluorine binding site 3 out of 3 in the PRMT5:MEP50 Complexed with 5,5-Bicyclic Inhibitor Compound 72


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of PRMT5:MEP50 Complexed with 5,5-Bicyclic Inhibitor Compound 72 within 5.0Å range: probe atom residue distance (Å) B Occ A:F705 b:30.0 occ:1.00 F A:WFV705 0.0 30.0 1.0 C7 A:WFV705 1.3 29.7 1.0 C8 A:WFV705 2.4 29.9 1.0 C6 A:WFV705 2.5 29.7 1.0 SG A:CYS449 3.0 38.6 1.0 CD2 A:LEU315 3.2 40.8 1.0 N3 A:WFV705 3.2 29.4 1.0 C9 A:WFV705 3.2 29.8 1.0 O A:HOH945 3.3 38.6 1.0 CB A:LEU315 3.3 33.0 1.0 CG A:LEU315 3.5 37.8 1.0 N A:WFV705 3.5 30.4 1.0 C5 A:WFV705 3.6 30.0 1.0 CA A:LEU315 3.7 32.9 1.0 CD2 A:LEU436 4.2 33.5 1.0 N A:LEU315 4.2 33.0 1.0 CB A:CYS449 4.5 34.7 1.0 N1 A:WFV705 4.6 30.1 1.0 N2 A:WFV705 4.9 30.0 1.0 C A:PRO314 4.9 36.5 1.0 C3 A:WFV705 4.9 31.3 1.0 O A:GLU444 5.0 28.9 1.0 CD1 A:LEU315 5.0 37.8 1.0

R.V.Quiroz, M.H.Reutershan, S.E.Schneider, D.Sloman, B.M.Lacey, B.M.Swalm, C.S.Yeung, C.Gibeau, D.S.Spellman, D.A.Rankic, D.Chen, D.Witter, D.Linn, E.Munsell, G.Feng, H.Xu, J.M.E.Hughes, J.Lim, J.Sauri, K.Geddes, M.Wan, M.S.Mansueto, N.E.Follmer, P.S.Fier, P.Siliphaivanh, P.Daublain, R.L.Palte, R.P.Hayes, S.Lee, S.Kawamura, S.Silverman, S.Sanyal, T.J.Henderson, Y.Ye, Y.Gao, B.Nicholson, M.R.Machacek. The Discovery of Two Novel Classes of 5,5-Bicyclic Nucleoside-Derived PRMT5 Inhibitors For the Treatment of Cancer. J.Med.Chem. V. 64 3911 2021.
ISSN: ISSN 0022-2623
PubMed: 33755451
DOI: 10.1021/ACS.JMEDCHEM.0C02083