Fluorine in PDB 8ea7: NKG2D Complexed with Inhibitor 3G

The structure of NKG2D Complexed with Inhibitor 3G, PDB code: 8ea7 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)	39.35 / 1.28
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	100.582, 43.138, 67.545, 90, 107.42, 90
R / Rfree (%)	19.3 / 21.5

The binding sites of Fluorine atom in the NKG2D Complexed with Inhibitor 3G (pdb code 8ea7). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 6 binding sites of Fluorine where determined in the NKG2D Complexed with Inhibitor 3G, PDB code: 8ea7:
Jump to Fluorine binding site number: 1; 2; 3; 4; 5; 6;

Fluorine binding site 1 out of 6 in the NKG2D Complexed with Inhibitor 3G


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 3G within 5.0Å range: probe atom residue distance (Å) B Occ A:F302 b:24.6 occ:0.76 F23 A:VMH302 0.0 24.6 0.8 C22 A:VMH302 1.4 25.0 0.8 F24 A:VMH302 2.2 26.0 0.8 F25 A:VMH302 2.2 30.2 0.8 C19 A:VMH302 2.4 15.3 0.8 C18 A:VMH302 2.8 16.8 0.8 F39 A:VMH302 3.2 24.8 0.8 F41 A:VMH302 3.3 26.9 0.8 C20 A:VMH302 3.6 15.8 0.8 CD1 B:ILE104 3.6 28.0 1.0 C38 A:VMH302 3.8 23.9 0.8 CB B:TYR111 3.8 17.8 1.0 C17 A:VMH302 4.1 16.6 0.8 CD1 B:LEU145 4.2 21.3 1.0 CG B:TYR111 4.4 16.3 1.0 CG2 B:ILE104 4.5 25.3 1.0 C36 A:VMH302 4.5 18.2 0.8 CB B:ILE104 4.6 19.9 1.0 CG1 B:ILE104 4.7 25.8 1.0 C21 A:VMH302 4.8 17.9 0.8 CG2 B:VAL149 4.8 18.1 1.0 CD2 B:TYR111 4.9 17.9 1.0 F40 A:VMH302 4.9 29.3 0.8 C16 A:VMH302 5.0 16.1 0.8

Fluorine binding site 2 out of 6 in the NKG2D Complexed with Inhibitor 3G


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 3G within 5.0Å range: probe atom residue distance (Å) B Occ A:F302 b:26.0 occ:0.76 F24 A:VMH302 0.0 26.0 0.8 C22 A:VMH302 1.4 25.0 0.8 F25 A:VMH302 2.1 30.2 0.8 F23 A:VMH302 2.2 24.6 0.8 C19 A:VMH302 2.4 15.3 0.8 C20 A:VMH302 2.8 15.8 0.8 C18 A:VMH302 3.6 16.8 0.8 CG2 B:ILE210 3.8 19.8 1.0 CB B:TYR111 3.9 17.8 1.0 CD1 B:ILE210 3.9 19.0 1.0 CG2 B:VAL149 4.0 18.1 1.0 C21 A:VMH302 4.2 17.9 0.8 CG B:TYR111 4.3 16.3 1.0 CD1 B:TYR111 4.3 17.0 1.0 CG1 B:ILE210 4.3 17.3 1.0 F41 A:VMH302 4.4 26.9 0.8 CD2 B:LEU146 4.6 18.2 1.0 C17 A:VMH302 4.7 16.6 0.8 CB B:ILE210 4.7 16.4 1.0 C16 A:VMH302 5.0 16.1 0.8

Fluorine binding site 3 out of 6 in the NKG2D Complexed with Inhibitor 3G


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 3G within 5.0Å range: probe atom residue distance (Å) B Occ A:F302 b:30.2 occ:0.76 F25 A:VMH302 0.0 30.2 0.8 C22 A:VMH302 1.4 25.0 0.8 F24 A:VMH302 2.1 26.0 0.8 F23 A:VMH302 2.2 24.6 0.8 C19 A:VMH302 2.4 15.3 0.8 C20 A:VMH302 3.1 15.8 0.8 C18 A:VMH302 3.3 16.8 0.8 CB B:TYR111 3.3 17.8 1.0 N B:PHE113 3.7 19.6 1.0 N B:GLN112 3.8 18.3 1.0 C B:TYR111 3.8 17.8 1.0 C B:GLN112 3.8 18.6 1.0 CA B:GLN112 4.0 19.5 1.0 O B:TYR111 4.1 16.6 1.0 CA B:TYR111 4.2 16.1 1.0 CG2 B:ILE210 4.2 19.8 1.0 CB B:PHE113 4.3 19.8 1.0 O B:GLN112 4.4 19.8 1.0 CD1 B:ILE104 4.4 28.0 1.0 CA B:PHE113 4.4 19.9 1.0 C21 A:VMH302 4.4 17.9 0.8 CG B:TYR111 4.4 16.3 1.0 C17 A:VMH302 4.5 16.6 0.8 O4 B:PEG301 4.7 24.7 1.0 CD1 B:TYR111 4.9 17.0 1.0 CG1 B:ILE210 4.9 17.3 1.0 C4 B:PEG301 4.9 30.6 1.0 C16 A:VMH302 5.0 16.1 0.8

Fluorine binding site 4 out of 6 in the NKG2D Complexed with Inhibitor 3G


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 3G within 5.0Å range: probe atom residue distance (Å) B Occ A:F302 b:24.8 occ:0.76 F39 A:VMH302 0.0 24.8 0.8 C38 A:VMH302 1.4 23.9 0.8 F41 A:VMH302 2.2 26.9 0.8 F40 A:VMH302 2.2 29.3 0.8 C36 A:VMH302 2.4 18.2 0.8 C35 A:VMH302 2.8 19.8 0.8 CD1 A:ILE104 3.2 36.8 1.0 F23 A:VMH302 3.2 24.6 0.8 CD1 B:LEU145 3.6 21.3 1.0 C37 A:VMH302 3.6 19.3 0.8 CD1 B:ILE104 3.7 28.0 1.0 CG1 A:ILE104 4.0 25.9 1.0 CG2 B:ILE104 4.1 25.3 1.0 C18 A:VMH302 4.1 16.8 0.8 C34 A:VMH302 4.2 19.8 0.8 C22 A:VMH302 4.4 25.0 0.8 CG B:LEU145 4.5 19.1 1.0 CG2 A:ILE104 4.6 26.9 1.0 CG1 B:ILE104 4.6 25.8 1.0 C19 A:VMH302 4.7 15.3 0.8 CB B:LEU145 4.8 19.2 1.0 C32 A:VMH302 4.8 17.9 0.8 CB B:ILE104 4.8 19.9 1.0 CB A:ILE104 5.0 22.9 1.0 C33 A:VMH302 5.0 17.4 0.8

Fluorine binding site 5 out of 6 in the NKG2D Complexed with Inhibitor 3G


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 3G within 5.0Å range: probe atom residue distance (Å) B Occ A:F302 b:29.3 occ:0.76 F40 A:VMH302 0.0 29.3 0.8 C38 A:VMH302 1.4 23.9 0.8 F39 A:VMH302 2.2 24.8 0.8 F41 A:VMH302 2.2 26.9 0.8 C36 A:VMH302 2.3 18.2 0.8 CD1 A:ILE104 2.7 36.8 1.0 C37 A:VMH302 3.1 19.3 0.8 C35 A:VMH302 3.3 19.8 0.8 CD1 B:LEU148 3.9 31.4 1.0 CG1 A:ILE104 4.0 25.9 1.0 CB B:LEU148 4.0 23.1 1.0 CB B:LEU145 4.0 19.2 1.0 O B:LEU145 4.0 16.5 1.0 CD1 B:LEU145 4.1 21.3 1.0 CE1 A:PHE113 4.3 25.7 1.0 CG B:LEU145 4.3 19.1 1.0 C32 A:VMH302 4.4 17.9 0.8 C34 A:VMH302 4.5 19.8 0.8 CG B:LEU148 4.5 26.7 1.0 CA B:LEU145 4.7 17.2 1.0 CD1 A:PHE113 4.7 23.4 1.0 C B:LEU145 4.7 16.0 1.0 F23 A:VMH302 4.9 24.6 0.8 C33 A:VMH302 4.9 17.4 0.8

Fluorine binding site 6 out of 6 in the NKG2D Complexed with Inhibitor 3G


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 3G within 5.0Å range: probe atom residue distance (Å) B Occ A:F302 b:26.9 occ:0.76 F41 A:VMH302 0.0 26.9 0.8 C38 A:VMH302 1.4 23.9 0.8 F39 A:VMH302 2.2 24.8 0.8 F40 A:VMH302 2.2 29.3 0.8 C36 A:VMH302 2.4 18.2 0.8 C37 A:VMH302 2.8 19.3 0.8 F23 A:VMH302 3.3 24.6 0.8 C35 A:VMH302 3.6 19.8 0.8 C18 A:VMH302 3.6 16.8 0.8 CG2 B:VAL149 3.8 18.1 1.0 O B:LEU145 3.8 16.5 1.0 CD1 B:LEU145 4.0 21.3 1.0 C19 A:VMH302 4.0 15.3 0.8 C22 A:VMH302 4.1 25.0 0.8 C32 A:VMH302 4.2 17.9 0.8 CG B:LEU145 4.2 19.1 1.0 C17 A:VMH302 4.3 16.6 0.8 F24 A:VMH302 4.4 26.0 0.8 CB B:LEU145 4.5 19.2 1.0 CB B:LEU148 4.5 23.1 1.0 O9 A:VMH302 4.5 16.7 0.8 CD1 A:ILE104 4.6 36.8 1.0 C B:LEU145 4.6 16.0 1.0 N B:VAL149 4.7 17.3 1.0 C34 A:VMH302 4.7 19.8 0.8 C B:LEU148 4.7 18.9 1.0 CA B:VAL149 4.8 17.6 1.0 O B:LEU148 4.9 21.6 1.0 CB B:VAL149 4.9 17.6 1.0 C33 A:VMH302 5.0 17.4 0.8 C20 A:VMH302 5.0 15.8 0.8

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