Fluorine in PDB 8eab: NKG2D Complexed with Inhibitor 4F

The structure of NKG2D Complexed with Inhibitor 4F, PDB code: 8eab was solved by A.A.Thompson, J.C.Grant, N.K.Karpowich, S.Sharma, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	34.03 / 1.44
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	101.621, 42.874, 67.881, 90, 107.87, 90
R / Rfree (%)	19.9 / 22.6

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>>> Page 1 <<< Page 2, Binding sites: 11 - 18;

Binding sites:

The binding sites of Fluorine atom in the NKG2D Complexed with Inhibitor 4F (pdb code 8eab). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 18 binding sites of Fluorine where determined in the NKG2D Complexed with Inhibitor 4F, PDB code: 8eab:
Jump to Fluorine binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Fluorine binding site 1 out of 18 in the NKG2D Complexed with Inhibitor 4F


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of NKG2D Complexed with Inhibitor 4F within 5.0Å range: probe atom residue distance (Å) B Occ B:F302 b:25.9 occ:0.46 F21 B:VN2302 0.0 25.9 0.5 F23 B:VN2302 1.1 22.0 0.5 F21 B:VN2302 1.2 22.2 0.5 C20 B:VN2302 1.2 23.9 0.5 C20 B:VN2302 1.4 23.9 0.5 F23 B:VN2302 2.2 25.3 0.5 F22 B:VN2302 2.2 21.9 0.5 C17 B:VN2302 2.3 20.3 0.5 C17 B:VN2302 2.4 20.3 0.5 F22 B:VN2302 2.4 29.1 0.5 C16 B:VN2302 3.0 20.6 0.5 C16 B:VN2302 3.1 20.6 0.5 F33 B:VN2302 3.1 30.5 0.5 C18 B:VN2302 3.3 20.8 0.5 C18 B:VN2302 3.5 20.7 0.5 CG2 B:VAL149 3.8 19.3 1.0 F31 B:VN2302 4.1 29.6 0.5 C30 B:VN2302 4.1 24.2 0.5 C26 B:VN2302 4.2 24.0 0.5 CB B:TYR111 4.3 18.4 1.0 C15 B:VN2302 4.3 19.9 0.5 C15 B:VN2302 4.4 19.9 0.5 C27 B:VN2302 4.5 22.6 0.5 CD1 B:ILE104 4.5 33.5 1.0 C19 B:VN2302 4.6 21.2 0.5 CG B:TYR111 4.6 15.4 1.0 CD2 B:LEU146 4.6 18.0 1.0 C19 B:VN2302 4.7 21.1 0.5 CD1 B:ILE210 4.7 17.3 1.0 CG2 B:ILE210 4.7 17.7 1.0 C28 B:VN2302 4.8 23.1 0.5 CD1 B:TYR111 4.8 15.3 1.0 CD1 B:LEU145 4.8 19.9 1.0 C25 B:VN2302 4.9 20.9 0.5

Fluorine binding site 2 out of 18 in the NKG2D Complexed with Inhibitor 4F


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of NKG2D Complexed with Inhibitor 4F within 5.0Å range: probe atom residue distance (Å) B Occ B:F302 b:22.2 occ:0.54 F21 B:VN2302 0.0 22.2 0.5 F21 B:VN2302 1.2 25.9 0.5 C20 B:VN2302 1.4 23.9 0.5 F22 B:VN2302 1.5 21.9 0.5 C20 B:VN2302 1.6 23.9 0.5 F23 B:VN2302 2.1 22.0 0.5 F22 B:VN2302 2.2 29.1 0.5 C17 B:VN2302 2.4 20.3 0.5 C17 B:VN2302 2.5 20.3 0.5 C16 B:VN2302 2.7 20.6 0.5 F23 B:VN2302 2.7 25.3 0.5 C16 B:VN2302 2.8 20.6 0.5 CG2 B:ILE210 3.5 17.7 1.0 CD1 B:ILE210 3.7 17.3 1.0 C18 B:VN2302 3.7 20.8 0.5 C18 B:VN2302 3.8 20.7 0.5 CG1 B:ILE210 3.9 17.7 1.0 C15 B:VN2302 4.1 19.9 0.5 C15 B:VN2302 4.1 19.9 0.5 CB B:TYR111 4.2 18.4 1.0 CG2 B:VAL149 4.2 19.3 1.0 F33 B:VN2302 4.3 30.5 0.5 CB B:ILE210 4.4 14.5 1.0 CD1 B:TYR111 4.5 15.3 1.0 CG B:TYR111 4.6 15.4 1.0 CD2 B:LEU146 4.7 18.0 1.0 C19 B:VN2302 4.8 21.2 0.5 C19 B:VN2302 4.9 21.1 0.5

Fluorine binding site 3 out of 18 in the NKG2D Complexed with Inhibitor 4F


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of NKG2D Complexed with Inhibitor 4F within 5.0Å range: probe atom residue distance (Å) B Occ B:F302 b:21.9 occ:0.46 F22 B:VN2302 0.0 21.9 0.5 F22 B:VN2302 0.9 29.1 0.5 C20 B:VN2302 1.3 23.9 0.5 C20 B:VN2302 1.4 23.9 0.5 F21 B:VN2302 1.5 22.2 0.5 F21 B:VN2302 2.2 25.9 0.5 F23 B:VN2302 2.2 25.3 0.5 C17 B:VN2302 2.3 20.3 0.5 C17 B:VN2302 2.3 20.3 0.5 F23 B:VN2302 2.4 22.0 0.5 C16 B:VN2302 3.0 20.6 0.5 C16 B:VN2302 3.0 20.6 0.5 C18 B:VN2302 3.4 20.7 0.5 C18 B:VN2302 3.4 20.8 0.5 CG2 B:ILE210 3.6 17.7 1.0 CB B:TYR111 3.7 18.4 1.0 N B:PHE113 3.9 18.5 1.0 C B:GLN112 4.0 19.3 1.0 CB B:PHE113 4.1 18.4 1.0 CG1 B:ILE210 4.2 17.7 1.0 N B:GLN112 4.2 16.9 1.0 O B:GLN112 4.2 18.6 1.0 C15 B:VN2302 4.3 19.9 0.5 CA B:PHE113 4.3 18.2 1.0 C15 B:VN2302 4.3 19.9 0.5 C B:TYR111 4.4 17.5 1.0 CD1 B:ILE210 4.4 17.3 1.0 CA B:GLN112 4.4 19.2 1.0 CB B:ILE210 4.5 14.5 1.0 CG B:TYR111 4.6 15.4 1.0 C19 B:VN2302 4.6 21.1 0.5 C19 B:VN2302 4.6 21.2 0.5 CA B:TYR111 4.6 16.6 1.0 CD1 B:TYR111 4.8 15.3 1.0 O B:TYR111 4.9 17.6 1.0 C14 B:VN2302 4.9 20.2 0.5 C14 B:VN2302 5.0 20.1 0.5

Fluorine binding site 4 out of 18 in the NKG2D Complexed with Inhibitor 4F


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 4 of NKG2D Complexed with Inhibitor 4F within 5.0Å range: probe atom residue distance (Å) B Occ B:F302 b:29.1 occ:0.54 F22 B:VN2302 0.0 29.1 0.5 F22 B:VN2302 0.9 21.9 0.5 C20 B:VN2302 1.3 23.9 0.5 C20 B:VN2302 1.4 23.9 0.5 F23 B:VN2302 1.5 25.3 0.5 F21 B:VN2302 2.2 22.2 0.5 F23 B:VN2302 2.2 22.0 0.5 C17 B:VN2302 2.3 20.3 0.5 C17 B:VN2302 2.4 20.3 0.5 F21 B:VN2302 2.4 25.9 0.5 C18 B:VN2302 3.1 20.7 0.5 C18 B:VN2302 3.1 20.8 0.5 C16 B:VN2302 3.3 20.6 0.5 C16 B:VN2302 3.3 20.6 0.5 CB B:TYR111 3.6 18.4 1.0 N B:PHE113 3.8 18.5 1.0 C B:GLN112 4.0 19.3 1.0 CB B:PHE113 4.1 18.4 1.0 N B:GLN112 4.1 16.9 1.0 C B:TYR111 4.1 17.5 1.0 CA B:GLN112 4.2 19.2 1.0 CA B:PHE113 4.3 18.2 1.0 C19 B:VN2302 4.3 21.1 0.5 CG2 B:ILE210 4.4 17.7 1.0 O B:TYR111 4.4 17.6 1.0 C19 B:VN2302 4.4 21.2 0.5 O4 B:PEG303 4.4 31.4 1.0 CD1 B:ILE104 4.4 33.5 1.0 O B:GLN112 4.5 18.6 1.0 C15 B:VN2302 4.5 19.9 0.5 C15 B:VN2302 4.5 19.9 0.5 CA B:TYR111 4.5 16.6 1.0 C4 B:PEG303 4.6 38.0 1.0 CG B:TYR111 4.7 15.4 1.0 CG1 B:ILE104 4.7 31.6 1.0 F33 B:VN2302 4.8 30.5 0.5 C14 B:VN2302 4.9 20.2 0.5 CG1 B:ILE210 5.0 17.7 1.0 C14 B:VN2302 5.0 20.1 0.5

Fluorine binding site 5 out of 18 in the NKG2D Complexed with Inhibitor 4F


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 5 of NKG2D Complexed with Inhibitor 4F within 5.0Å range: probe atom residue distance (Å) B Occ B:F302 b:25.3 occ:0.46 F23 B:VN2302 0.0 25.3 0.5 F23 B:VN2302 1.3 22.0 0.5 C20 B:VN2302 1.4 23.9 0.5 F22 B:VN2302 1.5 29.1 0.5 C20 B:VN2302 1.5 23.9 0.5 F21 B:VN2302 2.2 25.9 0.5 F22 B:VN2302 2.2 21.9 0.5 C17 B:VN2302 2.4 20.3 0.5 C17 B:VN2302 2.4 20.3 0.5 C18 B:VN2302 2.7 20.8 0.5 C18 B:VN2302 2.7 20.7 0.5 F21 B:VN2302 2.7 22.2 0.5 CD1 B:ILE104 3.3 33.5 1.0 F31 B:VN2302 3.5 29.6 0.5 F33 B:VN2302 3.7 30.5 0.5 C16 B:VN2302 3.7 20.6 0.5 C16 B:VN2302 3.8 20.6 0.5 CG1 B:ILE104 3.9 31.6 1.0 C27 B:VN2302 3.9 22.6 0.5 CB B:TYR111 4.0 18.4 1.0 C30 B:VN2302 4.0 24.2 0.5 C19 B:VN2302 4.1 21.2 0.5 C19 B:VN2302 4.1 21.1 0.5 F32 B:VN2302 4.2 24.8 0.5 C28 B:VN2302 4.3 23.1 0.5 C26 B:VN2302 4.3 24.0 0.5 C28 B:VN2302 4.4 22.6 0.5 C27 B:VN2302 4.5 23.2 0.5 CG2 B:ILE104 4.5 30.8 1.0 C4 B:PEG303 4.7 38.0 1.0 C30 B:VN2302 4.7 24.9 0.5 C15 B:VN2302 4.8 19.9 0.5 F31 B:VN2302 4.8 22.2 0.5 O B:TYR111 4.8 17.6 1.0 O4 B:PEG303 4.8 31.4 1.0 C15 B:VN2302 4.8 19.9 0.5 CG B:TYR111 4.8 15.4 1.0 C B:TYR111 4.8 17.5 1.0 CB B:ILE104 4.9 30.8 1.0 C14 B:VN2302 5.0 20.2 0.5 C29 B:VN2302 5.0 21.9 0.5

Fluorine binding site 6 out of 18 in the NKG2D Complexed with Inhibitor 4F


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 6 of NKG2D Complexed with Inhibitor 4F within 5.0Å range: probe atom residue distance (Å) B Occ B:F302 b:22.0 occ:0.54 F23 B:VN2302 0.0 22.0 0.5 F21 B:VN2302 1.1 25.9 0.5 F23 B:VN2302 1.3 25.3 0.5 C20 B:VN2302 1.3 23.9 0.5 C20 B:VN2302 1.4 23.9 0.5 F21 B:VN2302 2.1 22.2 0.5 F22 B:VN2302 2.2 29.1 0.5 F22 B:VN2302 2.4 21.9 0.5 C17 B:VN2302 2.4 20.3 0.5 C17 B:VN2302 2.4 20.3 0.5 F33 B:VN2302 2.8 30.5 0.5 C18 B:VN2302 3.0 20.8 0.5 C18 B:VN2302 3.1 20.7 0.5 F31 B:VN2302 3.2 29.6 0.5 C30 B:VN2302 3.4 24.2 0.5 C16 B:VN2302 3.5 20.6 0.5 CD1 B:ILE104 3.5 33.5 1.0 C16 B:VN2302 3.6 20.6 0.5 C27 B:VN2302 3.7 22.6 0.5 C26 B:VN2302 3.7 24.0 0.5 C28 B:VN2302 4.0 23.1 0.5 CB B:TYR111 4.2 18.4 1.0 C19 B:VN2302 4.3 21.2 0.5 CG1 B:ILE104 4.4 31.6 1.0 C19 B:VN2302 4.4 21.1 0.5 CD1 B:LEU145 4.5 19.9 1.0 C28 B:VN2302 4.5 22.6 0.5 CG2 B:VAL149 4.5 19.3 1.0 C27 B:VN2302 4.6 23.2 0.5 F32 B:VN2302 4.6 27.5 0.5 CG B:TYR111 4.6 15.4 1.0 C25 B:VN2302 4.6 20.9 0.5 C29 B:VN2302 4.7 21.9 0.5 C15 B:VN2302 4.7 19.9 0.5 C15 B:VN2302 4.7 19.9 0.5 F32 B:VN2302 4.9 24.8 0.5

Fluorine binding site 7 out of 18 in the NKG2D Complexed with Inhibitor 4F


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 7 of NKG2D Complexed with Inhibitor 4F within 5.0Å range: probe atom residue distance (Å) B Occ B:F302 b:22.2 occ:0.46 F31 B:VN2302 0.0 22.2 0.5 C30 B:VN2302 1.4 24.9 0.5 C27 B:VN2302 1.9 23.2 0.5 F32 B:VN2302 2.2 24.8 0.5 F33 B:VN2302 2.2 25.9 0.5 C28 B:VN2302 2.4 22.6 0.5 C26 B:VN2302 2.6 24.6 0.5 C27 B:VN2302 2.8 22.6 0.5 F31 B:VN2302 3.0 29.6 0.5 C28 B:VN2302 3.1 23.1 0.5 CD1 A:ILE104 3.5 29.9 1.0 C30 B:VN2302 3.5 24.2 0.5 F49 B:VN2302 3.6 25.3 0.5 CD1 A:LEU145 3.6 21.4 1.0 C29 B:VN2302 3.6 21.2 0.5 CD1 B:ILE104 3.7 33.5 1.0 F49 B:VN2302 3.8 21.4 0.5 C25 B:VN2302 3.9 21.9 0.5 CG2 A:ILE104 4.0 24.0 1.0 C26 B:VN2302 4.2 24.0 0.5 CG2 B:ILE104 4.2 30.8 1.0 F32 B:VN2302 4.2 27.5 0.5 C29 B:VN2302 4.3 21.9 0.5 CG A:LEU145 4.5 20.1 1.0 CB B:ILE104 4.6 30.8 1.0 C24 B:VN2302 4.6 21.2 0.5 CG1 A:ILE104 4.6 18.3 1.0 F33 B:VN2302 4.7 30.5 0.5 C44 B:VN2302 4.7 21.6 0.5 C44 B:VN2302 4.7 21.7 0.5 CG1 B:ILE104 4.8 31.6 1.0 C24 B:VN2302 4.8 22.4 0.5 CB A:LEU145 4.8 21.1 1.0 F23 B:VN2302 4.8 25.3 0.5 CB A:ILE104 4.8 18.9 1.0 C46 B:VN2302 4.8 21.4 0.5 C46 B:VN2302 5.0 21.1 0.5 C25 B:VN2302 5.0 20.9 0.5

Fluorine binding site 8 out of 18 in the NKG2D Complexed with Inhibitor 4F


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 8 of NKG2D Complexed with Inhibitor 4F within 5.0Å range: probe atom residue distance (Å) B Occ B:F302 b:29.6 occ:0.54 F31 B:VN2302 0.0 29.6 0.5 C30 B:VN2302 1.4 24.2 0.5 C27 B:VN2302 1.8 22.6 0.5 F32 B:VN2302 2.2 27.5 0.5 F33 B:VN2302 2.2 30.5 0.5 C28 B:VN2302 2.4 23.1 0.5 C26 B:VN2302 2.6 24.0 0.5 C27 B:VN2302 2.7 23.2 0.5 CD1 B:ILE104 2.8 33.5 1.0 F31 B:VN2302 3.0 22.2 0.5 C28 B:VN2302 3.0 22.6 0.5 CD1 A:ILE104 3.1 29.9 1.0 F23 B:VN2302 3.2 22.0 0.5 C30 B:VN2302 3.4 24.9 0.5 CD1 B:LEU145 3.5 19.9 1.0 F23 B:VN2302 3.5 25.3 0.5 C29 B:VN2302 3.7 21.9 0.5 C25 B:VN2302 3.9 20.9 0.5 F21 B:VN2302 4.1 25.9 0.5 F32 B:VN2302 4.1 24.8 0.5 C26 B:VN2302 4.1 24.6 0.5 C29 B:VN2302 4.2 21.2 0.5 CG1 A:ILE104 4.2 18.3 1.0 CG B:LEU145 4.2 16.8 1.0 CG1 B:ILE104 4.3 31.6 1.0 C20 B:VN2302 4.3 23.9 0.5 C20 B:VN2302 4.5 23.9 0.5 CB B:LEU145 4.6 18.3 1.0 C24 B:VN2302 4.6 22.4 0.5 F33 B:VN2302 4.6 25.9 0.5 C18 B:VN2302 4.7 20.8 0.5 C18 B:VN2302 4.8 20.7 0.5 C24 B:VN2302 4.8 21.2 0.5 CG2 A:ILE104 4.9 24.0 1.0 C17 B:VN2302 4.9 20.3 0.5 C17 B:VN2302 4.9 20.3 0.5 C25 B:VN2302 4.9 21.9 0.5

Fluorine binding site 9 out of 18 in the NKG2D Complexed with Inhibitor 4F


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 9 of NKG2D Complexed with Inhibitor 4F within 5.0Å range: probe atom residue distance (Å) B Occ B:F302 b:24.8 occ:0.46 F32 B:VN2302 0.0 24.8 0.5 C30 B:VN2302 1.4 24.9 0.5 C26 B:VN2302 2.2 24.6 0.5 F33 B:VN2302 2.2 25.9 0.5 F31 B:VN2302 2.2 22.2 0.5 C27 B:VN2302 2.3 23.2 0.5 C28 B:VN2302 2.4 22.6 0.5 C29 B:VN2302 3.1 21.2 0.5 C25 B:VN2302 3.2 21.9 0.5 C27 B:VN2302 3.3 22.6 0.5 C28 B:VN2302 3.5 23.1 0.5 CD1 A:LEU148 3.9 26.5 1.0 C18 B:VN2302 3.9 20.7 0.5 C18 B:VN2302 4.0 20.8 0.5 F31 B:VN2302 4.1 29.6 0.5 CG2 B:ILE104 4.1 30.8 1.0 CB A:LEU145 4.1 21.1 1.0 C24 B:VN2302 4.1 21.2 0.5 C29 B:VN2302 4.2 21.9 0.5 CB A:LEU148 4.2 17.7 1.0 CD1 A:LEU145 4.2 21.4 1.0 O A:LEU145 4.2 17.0 1.0 F23 B:VN2302 4.2 25.3 0.5 C30 B:VN2302 4.4 24.2 0.5 C24 B:VN2302 4.4 22.4 0.5 C19 B:VN2302 4.4 21.2 0.5 C19 B:VN2302 4.4 21.1 0.5 C3 B:PEG303 4.5 38.0 1.0 CG A:LEU145 4.5 20.1 1.0 C26 B:VN2302 4.5 24.0 0.5 CD1 B:ILE104 4.5 33.5 1.0 CG A:LEU148 4.6 20.0 1.0 CA A:LEU145 4.8 18.6 1.0 C4 B:PEG303 4.8 38.0 1.0 C A:LEU145 4.9 15.8 1.0 F23 B:VN2302 4.9 22.0 0.5 C25 B:VN2302 4.9 20.9 0.5

Fluorine binding site 10 out of 18 in the NKG2D Complexed with Inhibitor 4F


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 10 of NKG2D Complexed with Inhibitor 4F within 5.0Å range: probe atom residue distance (Å) B Occ B:F302 b:27.5 occ:0.54 F32 B:VN2302 0.0 27.5 0.5 C30 B:VN2302 1.4 24.2 0.5 C26 B:VN2302 2.0 24.0 0.5 F31 B:VN2302 2.2 29.6 0.5 F33 B:VN2302 2.2 30.5 0.5 C27 B:VN2302 2.2 22.6 0.5 C28 B:VN2302 2.4 23.1 0.5 C29 B:VN2302 3.1 21.9 0.5 CD1 A:ILE104 3.2 29.9 1.0 C25 B:VN2302 3.2 20.9 0.5 C27 B:VN2302 3.3 23.2 0.5 C28 B:VN2302 3.4 22.6 0.5 O B:LEU145 3.7 17.1 1.0 CB B:LEU145 3.8 18.3 1.0 CD1 B:LEU145 4.1 19.9 1.0 CG B:LEU145 4.1 16.8 1.0 CB B:LEU148 4.1 19.0 1.0 C24 B:VN2302 4.1 22.4 0.5 C44 B:VN2302 4.2 21.7 0.5 F31 B:VN2302 4.2 22.2 0.5 C29 B:VN2302 4.2 21.2 0.5 C44 B:VN2302 4.2 21.6 0.5 CD1 B:LEU148 4.2 22.1 1.0 C45 B:VN2302 4.4 18.9 0.5 C45 B:VN2302 4.4 18.9 0.5 C30 B:VN2302 4.4 24.9 0.5 C B:LEU145 4.4 15.7 1.0 C24 B:VN2302 4.4 21.2 0.5 CA B:LEU145 4.4 15.5 1.0 CG1 A:ILE104 4.4 18.3 1.0 C26 B:VN2302 4.5 24.6 0.5 F23 B:VN2302 4.6 22.0 0.5 CG B:LEU148 4.7 21.4 1.0 CD1 B:ILE104 4.9 33.5 1.0 C25 B:VN2302 5.0 21.9 0.5

A.A.Thompson, M.B.Harbut, P.P.Kung, N.K.Karpowich, J.D.Branson, J.C.Grant, D.Hagan, H.A.Pascual, G.Bai, R.B.Zavareh, H.R.Coate, B.C.Collins, M.Cote, C.F.Gelin, K.L.Damm-Ganamet, H.Gholami, A.R.Huff, L.Limon, K.J.Lumb, P.A.Mak, K.M.Nakafuku, E.V.Price, A.Y.Shih, M.Tootoonchi, N.A.Vellore, J.Wang, N.Wei, J.Ziff, S.B.Berger, J.P.Edwards, A.Gardet, S.Sun, J.E.Towne, J.D.Venable, Z.Shi, H.Venkatesan, M.L.Rives, S.Sharma, B.T.Shireman, S.J.Allen. Identification of Small-Molecule Protein-Protein Interaction Inhibitors For NKG2D Proc.Natl.Acad.Sci.Usa V. 120 2023.
ISSN: ESSN 1091-6490
DOI: 10.1073/PNAS.2216342120