Fluorine in PDB 8ea6: NKG2D Complexed with Inhibitor 3E

The structure of NKG2D Complexed with Inhibitor 3E, PDB code: 8ea6 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)	33.90 / 1.73
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	100.635, 44.675, 64.953, 90, 106.18, 90
R / Rfree (%)	18.6 / 21.5

The binding sites of Fluorine atom in the NKG2D Complexed with Inhibitor 3E (pdb code 8ea6). 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 3E, PDB code: 8ea6:
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 3E


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 3E within 5.0Å range: probe atom residue distance (Å) B Occ B:F301 b:29.6 occ:0.91 F23 B:VMB301 0.0 29.6 0.9 C22 B:VMB301 1.4 28.1 0.9 F24 B:VMB301 2.1 31.9 0.9 F25 B:VMB301 2.2 27.3 0.9 C19 B:VMB301 2.4 18.1 0.9 C18 B:VMB301 2.8 18.3 0.9 C20 B:VMB301 3.6 16.1 0.9 CD1 A:ILE210 3.7 16.8 1.0 CG2 A:ILE210 3.7 21.5 1.0 CG2 A:VAL149 3.8 20.5 1.0 CB A:TYR111 4.1 23.3 1.0 CG1 A:ILE210 4.2 18.9 1.0 C17 B:VMB301 4.2 18.0 0.9 F35 B:VMB301 4.5 31.2 0.9 CD2 A:TYR111 4.6 24.0 1.0 CG A:TYR111 4.6 24.4 1.0 CB A:ILE210 4.6 21.0 1.0 CD2 A:LEU146 4.6 20.0 1.0 C21 B:VMB301 4.7 19.9 0.9 C16 B:VMB301 5.0 20.3 0.9

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


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 3E within 5.0Å range: probe atom residue distance (Å) B Occ B:F301 b:31.9 occ:0.91 F24 B:VMB301 0.0 31.9 0.9 C22 B:VMB301 1.3 28.1 0.9 F25 B:VMB301 2.1 27.3 0.9 F23 B:VMB301 2.1 29.6 0.9 C19 B:VMB301 2.4 18.1 0.9 C18 B:VMB301 3.2 18.3 0.9 C20 B:VMB301 3.2 16.1 0.9 N A:PHE113 3.7 26.1 1.0 CB A:TYR111 3.7 23.3 1.0 CD1 A:ILE104 3.8 30.1 1.0 C A:GLN112 3.8 26.6 1.0 N A:GLN112 3.9 24.0 1.0 C A:TYR111 4.0 27.4 1.0 CA A:GLN112 4.0 26.8 1.0 CB A:PHE113 4.1 25.9 1.0 CG2 A:ILE210 4.1 21.5 1.0 CA A:PHE113 4.2 27.9 1.0 O A:GLN112 4.3 22.9 1.0 O A:TYR111 4.4 25.0 1.0 C17 B:VMB301 4.4 18.0 0.9 C21 B:VMB301 4.5 19.9 0.9 CA A:TYR111 4.5 24.9 1.0 CG1 A:ILE210 4.7 18.9 1.0 CG A:TYR111 4.8 24.4 1.0 CD1 A:ILE210 4.9 16.8 1.0 C16 B:VMB301 5.0 20.3 0.9

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


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 3E within 5.0Å range: probe atom residue distance (Å) B Occ B:F301 b:27.3 occ:0.91 F25 B:VMB301 0.0 27.3 0.9 C22 B:VMB301 1.4 28.1 0.9 F24 B:VMB301 2.1 31.9 0.9 F23 B:VMB301 2.2 29.6 0.9 C19 B:VMB301 2.4 18.1 0.9 C20 B:VMB301 2.7 16.1 0.9 F33 B:VMB301 3.3 32.6 0.9 F35 B:VMB301 3.3 31.2 0.9 CD1 A:ILE104 3.4 30.1 1.0 C18 B:VMB301 3.6 18.3 0.9 C32 B:VMB301 3.9 29.9 0.9 CB A:TYR111 4.1 23.3 1.0 C21 B:VMB301 4.1 19.9 0.9 CD1 A:LEU145 4.3 30.5 1.0 CG2 A:VAL149 4.6 20.5 1.0 C30 B:VMB301 4.6 22.5 0.9 CG1 A:ILE104 4.7 28.9 1.0 CB A:ILE104 4.7 25.6 1.0 C17 B:VMB301 4.8 18.0 0.9 CG A:TYR111 4.8 24.4 1.0 CG2 A:ILE104 4.8 27.8 1.0 F34 B:VMB301 4.9 30.6 0.9 C16 B:VMB301 5.0 20.3 0.9

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


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 3E within 5.0Å range: probe atom residue distance (Å) B Occ B:F301 b:32.6 occ:0.91 F33 B:VMB301 0.0 32.6 0.9 C32 B:VMB301 1.4 29.9 0.9 F35 B:VMB301 2.1 31.2 0.9 F34 B:VMB301 2.2 30.6 0.9 C30 B:VMB301 2.4 22.5 0.9 C29 B:VMB301 2.7 19.1 0.9 F25 B:VMB301 3.3 27.3 0.9 C31 B:VMB301 3.6 17.4 0.9 CD1 A:LEU145 3.8 30.5 1.0 CD1 B:ILE104 3.9 39.6 1.0 CD1 A:ILE104 4.0 30.1 1.0 C20 B:VMB301 4.1 16.1 0.9 C28 B:VMB301 4.1 19.7 0.9 CG2 A:ILE104 4.1 27.8 1.0 CG2 B:ILE104 4.4 28.0 1.0 C22 B:VMB301 4.5 28.1 0.9 CG1 B:ILE104 4.5 33.4 1.0 CG1 A:ILE104 4.7 28.9 1.0 C19 B:VMB301 4.7 18.1 0.9 C26 B:VMB301 4.8 16.6 0.9 CG A:LEU145 4.8 25.2 1.0 CB A:ILE104 4.9 25.6 1.0 C27 B:VMB301 4.9 18.4 0.9 C21 B:VMB301 5.0 19.9 0.9

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


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 3E within 5.0Å range: probe atom residue distance (Å) B Occ B:F301 b:30.6 occ:0.91 F34 B:VMB301 0.0 30.6 0.9 C32 B:VMB301 1.3 29.9 0.9 F33 B:VMB301 2.2 32.6 0.9 F35 B:VMB301 2.2 31.2 0.9 C30 B:VMB301 2.4 22.5 0.9 CD1 B:ILE104 2.9 39.6 1.0 C31 B:VMB301 3.2 17.4 0.9 C29 B:VMB301 3.3 19.1 0.9 CD1 A:LEU148 3.6 33.9 1.0 CB A:LEU148 3.9 20.8 1.0 CG1 B:ILE104 4.0 33.4 1.0 CD1 A:LEU145 4.1 30.5 1.0 O A:LEU145 4.2 20.1 1.0 CB A:LEU145 4.2 24.9 1.0 CE1 B:PHE113 4.4 31.8 1.0 CG A:LEU148 4.4 25.5 1.0 C26 B:VMB301 4.5 16.6 0.9 CG A:LEU145 4.5 25.2 1.0 C28 B:VMB301 4.5 19.7 0.9 CD1 B:PHE113 4.7 33.2 1.0 CA A:LEU145 4.9 20.5 1.0 C A:LEU145 4.9 18.9 1.0 F25 B:VMB301 4.9 27.3 0.9 CG2 B:ILE104 5.0 28.0 1.0

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


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 3E within 5.0Å range: probe atom residue distance (Å) B Occ B:F301 b:31.2 occ:0.91 F35 B:VMB301 0.0 31.2 0.9 C32 B:VMB301 1.4 29.9 0.9 F33 B:VMB301 2.1 32.6 0.9 F34 B:VMB301 2.2 30.6 0.9 C30 B:VMB301 2.4 22.5 0.9 C31 B:VMB301 2.8 17.4 0.9 F25 B:VMB301 3.3 27.3 0.9 C29 B:VMB301 3.6 19.1 0.9 C20 B:VMB301 3.7 16.1 0.9 CG2 A:VAL149 3.8 20.5 1.0 O A:LEU145 3.9 20.1 1.0 CD1 A:LEU145 4.0 30.5 1.0 C19 B:VMB301 4.1 18.1 0.9 C22 B:VMB301 4.1 28.1 0.9 C26 B:VMB301 4.2 16.6 0.9 CB A:LEU148 4.3 20.8 1.0 CG A:LEU145 4.4 25.2 1.0 C21 B:VMB301 4.4 19.9 0.9 O9 B:VMB301 4.5 17.0 0.9 F23 B:VMB301 4.5 29.6 0.9 N A:VAL149 4.5 21.3 1.0 C A:LEU148 4.6 20.9 1.0 CA A:VAL149 4.7 21.8 1.0 C28 B:VMB301 4.7 19.7 0.9 CB A:LEU145 4.7 24.9 1.0 C A:LEU145 4.8 18.9 1.0 O A:LEU148 4.8 21.5 1.0 CB A:VAL149 4.9 19.8 1.0 CD1 B:ILE104 4.9 39.6 1.0 C27 B:VMB301 5.0 18.4 0.9

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