Fluorine in PDB 8qm6: Potential Drug Binding Sites For Translation Initiation Factor EIF4E

The structure of Potential Drug Binding Sites For Translation Initiation Factor EIF4E, PDB code: 8qm6 was solved by A.Cleasby, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	47.19 / 1.93
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	47.293, 69.344, 64.771, 90, 96.13, 90
R / Rfree (%)	18.7 / 22.7

The binding sites of Fluorine atom in the Potential Drug Binding Sites For Translation Initiation Factor EIF4E (pdb code 8qm6). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 4 binding sites of Fluorine where determined in the Potential Drug Binding Sites For Translation Initiation Factor EIF4E, PDB code: 8qm6:
Jump to Fluorine binding site number: 1; 2; 3; 4;

Fluorine binding site 1 out of 4 in the Potential Drug Binding Sites For Translation Initiation Factor EIF4E


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of Potential Drug Binding Sites For Translation Initiation Factor EIF4E within 5.0Å range: probe atom residue distance (Å) B Occ A:F303 b:20.4 occ:0.50 F16 A:W2N303 0.0 20.4 0.5 F17 A:W4B304 0.9 18.7 0.5 C15 A:W2N303 1.4 21.5 0.5 C16 A:W4B304 1.9 20.0 0.5 H23 A:W4B304 2.1 22.5 0.5 C14 A:W2N303 2.4 22.1 0.5 C10 A:W2N303 2.4 22.5 0.5 H24 A:W2N303 2.5 22.7 0.5 H29 A:W2N303 2.5 22.1 0.5 C7 A:W4B304 2.7 22.6 0.5 C11 A:W4B304 2.8 21.6 0.5 C15 A:W4B304 2.8 20.1 0.5 C7 A:W2N303 2.9 22.4 0.5 C8 A:W2N303 2.9 22.7 0.5 H29 A:W4B304 3.0 20.1 0.5 C8 A:W4B304 3.1 22.7 0.5 CD1 A:LEU45 3.1 27.0 1.0 CZ2 A:TRP130 3.1 19.0 1.0 NE1 A:TRP130 3.3 19.3 1.0 CE2 A:TRP130 3.5 18.7 1.0 C13 A:W2N303 3.6 22.3 0.5 C11 A:W2N303 3.6 22.6 0.5 CD2 A:LEU134 3.9 19.4 1.0 C6 A:W4B304 3.9 24.3 0.5 CD1 A:LEU134 4.0 18.4 1.0 C12 A:W4B304 4.0 22.1 0.5 C14 A:W4B304 4.0 20.9 0.5 C12 A:W2N303 4.1 22.7 0.5 C6 A:W2N303 4.1 23.7 0.5 C9 A:W2N303 4.1 23.6 0.5 H22 A:W4B304 4.2 24.3 0.5 CH2 A:TRP130 4.3 18.9 1.0 C9 A:W4B304 4.4 23.3 0.5 H28 A:W2N303 4.4 22.4 0.5 CG A:LEU45 4.4 27.4 1.0 H26 A:W2N303 4.4 22.6 0.5 CB A:TYR91 4.5 27.5 1.0 CD2 A:LEU45 4.5 28.9 1.0 H25 A:W2N303 4.5 23.6 0.5 C13 A:W4B304 4.5 21.8 0.5 H23 A:W2N303 4.5 23.6 0.5 CG A:LEU134 4.5 17.7 1.0 CD1 A:TRP130 4.6 17.7 1.0 CB A:LEU93 4.6 17.1 1.0 H26 A:W4B304 4.7 22.1 0.5 H28 A:W4B304 4.8 20.9 0.5 CD2 A:TRP130 4.9 16.8 1.0 H24 A:W4B304 4.9 23.3 0.5 N A:LEU93 4.9 19.1 1.0 C5 A:W4B304 5.0 25.2 0.5

Fluorine binding site 2 out of 4 in the Potential Drug Binding Sites For Translation Initiation Factor EIF4E


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of Potential Drug Binding Sites For Translation Initiation Factor EIF4E within 5.0Å range: probe atom residue distance (Å) B Occ A:F304 b:18.7 occ:0.50 F17 A:W4B304 0.0 18.7 0.5 F16 A:W2N303 0.9 20.4 0.5 C15 A:W2N303 1.1 21.5 0.5 C16 A:W4B304 1.4 20.0 0.5 C14 A:W2N303 2.1 22.1 0.5 C10 A:W2N303 2.1 22.5 0.5 C11 A:W4B304 2.3 21.6 0.5 C15 A:W4B304 2.4 20.1 0.5 H29 A:W2N303 2.4 22.1 0.5 H23 A:W4B304 2.5 22.5 0.5 H29 A:W4B304 2.5 20.1 0.5 C7 A:W2N303 2.8 22.4 0.5 C8 A:W4B304 2.8 22.7 0.5 C7 A:W4B304 2.9 22.6 0.5 H24 A:W2N303 3.0 22.7 0.5 CD1 A:LEU134 3.1 18.4 1.0 NE1 A:TRP130 3.1 19.3 1.0 C13 A:W2N303 3.2 22.3 0.5 C8 A:W2N303 3.2 22.7 0.5 C11 A:W2N303 3.2 22.6 0.5 CD2 A:LEU134 3.3 19.4 1.0 CZ2 A:TRP130 3.3 19.0 1.0 CE2 A:TRP130 3.4 18.7 1.0 C12 A:W4B304 3.6 22.1 0.5 C14 A:W4B304 3.6 20.9 0.5 C12 A:W2N303 3.7 22.7 0.5 CG A:LEU134 3.8 17.7 1.0 C6 A:W2N303 3.8 23.7 0.5 CD1 A:LEU45 3.9 27.0 1.0 H28 A:W2N303 4.0 22.4 0.5 C9 A:W4B304 4.0 23.3 0.5 H26 A:W2N303 4.0 22.6 0.5 C6 A:W4B304 4.1 24.3 0.5 H23 A:W2N303 4.1 23.6 0.5 C13 A:W4B304 4.1 21.8 0.5 CD1 A:TRP130 4.2 17.7 1.0 H26 A:W4B304 4.4 22.1 0.5 H28 A:W4B304 4.4 20.9 0.5 H24 A:W4B304 4.4 23.3 0.5 C9 A:W2N303 4.4 23.6 0.5 H22 A:W4B304 4.5 24.3 0.5 CH2 A:TRP130 4.5 18.9 1.0 H27 A:W2N303 4.6 22.7 0.5 CD2 A:TRP130 4.7 16.8 1.0 CB A:LEU93 4.8 17.1 1.0 C5 A:W2N303 4.9 24.4 0.5 C10 A:W4B304 4.9 24.4 0.5 C5 A:W4B304 5.0 25.2 0.5 H25 A:W2N303 5.0 23.6 0.5 CD2 A:LEU45 5.0 28.9 1.0

Fluorine binding site 3 out of 4 in the Potential Drug Binding Sites For Translation Initiation Factor EIF4E


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of Potential Drug Binding Sites For Translation Initiation Factor EIF4E within 5.0Å range: probe atom residue distance (Å) B Occ B:F504 b:18.1 occ:0.50 F17 B:W4B504 0.0 18.1 0.5 F16 B:W2N505 0.7 34.3 0.5 C15 B:W2N505 0.9 35.7 0.5 C16 B:W4B504 1.4 19.2 0.5 C10 B:W2N505 1.9 36.6 0.5 C14 B:W2N505 2.0 36.4 0.5 H29 B:W2N505 2.3 36.4 0.5 C15 B:W4B504 2.4 19.4 0.5 C11 B:W4B504 2.4 20.6 0.5 H24 B:W4B504 2.5 23.5 0.5 H29 B:W4B504 2.5 19.4 0.5 C7 B:W2N505 2.6 36.7 0.5 H23 B:W2N505 2.8 37.0 0.5 C8 B:W4B504 2.9 22.6 0.5 C9 B:W4B504 2.9 23.5 0.5 C6 B:W2N505 3.0 37.0 0.5 C11 B:W2N505 3.1 37.0 0.5 NE1 B:TRP130 3.1 23.4 1.0 C13 B:W2N505 3.1 37.0 0.5 CZ2 B:TRP130 3.3 23.5 1.0 CD1 B:LEU134 3.3 22.6 1.0 CE2 B:TRP130 3.4 22.5 1.0 CD2 B:LEU134 3.5 24.1 1.0 C12 B:W2N505 3.6 37.2 0.5 C14 B:W4B504 3.6 20.0 0.5 C12 B:W4B504 3.6 19.8 0.5 C8 B:W2N505 3.7 37.1 0.5 CD1 B:LEU45 3.7 28.4 1.0 H26 B:W2N505 3.9 37.0 0.5 H24 B:W2N505 3.9 37.1 0.5 H28 B:W2N505 3.9 37.0 0.5 CG B:LEU134 4.0 23.0 1.0 C7 B:W4B504 4.1 24.2 0.5 C10 B:W4B504 4.1 25.4 0.5 C13 B:W4B504 4.1 19.6 0.5 C5 B:W2N505 4.2 37.7 0.5 CD1 B:TRP130 4.3 23.2 1.0 H28 B:W4B504 4.4 20.0 0.5 H26 B:W4B504 4.4 19.8 0.5 CH2 B:TRP130 4.5 24.0 1.0 H23 B:W4B504 4.5 24.2 0.5 H25 B:W4B504 4.5 25.4 0.5 H27 B:W2N505 4.5 37.2 0.5 CD2 B:TRP130 4.7 20.6 1.0 C9 B:W2N505 4.7 37.2 0.5 H22 B:W2N505 4.8 37.7 0.5 CB B:LEU93 4.8 21.3 1.0 CD2 B:LEU45 4.8 28.7 1.0 CG B:LEU45 4.9 26.8 1.0 C4 B:W2N505 5.0 37.5 0.5 C6 B:W4B504 5.0 25.2 0.5

Fluorine binding site 4 out of 4 in the Potential Drug Binding Sites For Translation Initiation Factor EIF4E


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 4 of Potential Drug Binding Sites For Translation Initiation Factor EIF4E within 5.0Å range: probe atom residue distance (Å) B Occ B:F505 b:34.3 occ:0.50 F16 B:W2N505 0.0 34.3 0.5 F17 B:W4B504 0.7 18.1 0.5 C15 B:W2N505 1.4 35.7 0.5 C16 B:W4B504 1.9 19.2 0.5 H24 B:W4B504 2.3 23.5 0.5 C10 B:W2N505 2.3 36.6 0.5 C14 B:W2N505 2.4 36.4 0.5 H23 B:W2N505 2.5 37.0 0.5 H29 B:W2N505 2.5 36.4 0.5 C15 B:W4B504 2.8 19.4 0.5 C11 B:W4B504 2.8 20.6 0.5 C7 B:W2N505 2.8 36.7 0.5 H29 B:W4B504 2.9 19.4 0.5 C9 B:W4B504 2.9 23.5 0.5 C6 B:W2N505 2.9 37.0 0.5 CZ2 B:TRP130 2.9 23.5 1.0 NE1 B:TRP130 3.1 23.4 1.0 C8 B:W4B504 3.2 22.6 0.5 CE2 B:TRP130 3.3 22.5 1.0 CD1 B:LEU45 3.4 28.4 1.0 C11 B:W2N505 3.6 37.0 0.5 C13 B:W2N505 3.6 37.0 0.5 CD2 B:LEU134 3.7 24.1 1.0 CD1 B:LEU134 3.9 22.6 1.0 C8 B:W2N505 4.0 37.1 0.5 C10 B:W4B504 4.0 25.4 0.5 C14 B:W4B504 4.1 20.0 0.5 C12 B:W4B504 4.1 19.8 0.5 C5 B:W2N505 4.1 37.7 0.5 CH2 B:TRP130 4.1 24.0 1.0 C12 B:W2N505 4.1 37.2 0.5 H25 B:W4B504 4.3 25.4 0.5 CG B:LEU134 4.4 23.0 1.0 H26 B:W2N505 4.4 37.0 0.5 H28 B:W2N505 4.4 37.0 0.5 CD1 B:TRP130 4.4 23.2 1.0 H24 B:W2N505 4.4 37.1 0.5 C7 B:W4B504 4.4 24.2 0.5 CB B:TYR91 4.4 31.8 1.0 H22 B:W2N505 4.5 37.7 0.5 C13 B:W4B504 4.6 19.6 0.5 CB B:LEU93 4.6 21.3 1.0 CG B:LEU45 4.6 26.8 1.0 CD2 B:TRP130 4.6 20.6 1.0 CD2 B:LEU45 4.8 28.7 1.0 H28 B:W4B504 4.8 20.0 0.5 H26 B:W4B504 4.8 19.8 0.5 N B:LEU93 4.9 23.4 1.0 C9 B:W2N505 4.9 37.2 0.5 H23 B:W4B504 4.9 24.2 0.5 C4 B:W2N505 5.0 37.5 0.5

Y.S.Sharp, M.Martella, C.I.Milton, G.Ward, A.J.Woodhead, C.J.Richardson, M.G.Carr, E.Chiarparin, B.D.Cons, J.Coyle, S.D'agostino, C.E.East, S.D.Hiscock, C.Martinez-Fleites, P.N.Mortenson, N.Palmer, P.Pathuri, M.V.Powers, S.M.Saalau, J.D.St.Denis, K.Swabey, M.Vinkovic, G.Williams, P.A.Clarke. Integrating Fragment-Based Screening with Targeted Protein Degradation and Genetic Rescue to Explore EIF4E Function Nat Commun 2025.
ISSN: ESSN 2041-1723
DOI: 10.1038/S41467-024-54356-1