Fluorine in PDB 8ea8: NKG2D Complexed with Inhibitor 4A

The structure of NKG2D Complexed with Inhibitor 4A, PDB code: 8ea8 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)	37.25 / 1.77
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	100.09, 43.675, 72.591, 90, 125.01, 90
R / Rfree (%)	16.2 / 20

The binding sites of Fluorine atom in the NKG2D Complexed with Inhibitor 4A (pdb code 8ea8). 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 4A, PDB code: 8ea8:
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 4A


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 4A within 5.0Å range: probe atom residue distance (Å) B Occ B:F404 b:21.8 occ:1.00 F23 B:VML404 0.0 21.8 1.0 C22 B:VML404 1.3 20.8 1.0 F24 B:VML404 2.1 24.0 1.0 F25 B:VML404 2.1 19.9 1.0 C19 B:VML404 2.4 13.4 1.0 C18 B:VML404 2.8 14.2 1.0 C20 B:VML404 3.6 14.8 1.0 CG2 A:ILE210 3.6 9.5 1.0 CD1 A:ILE210 3.8 10.3 1.0 CG2 A:VAL149 3.9 12.2 1.0 CB A:TYR111 4.0 8.6 1.0 CG1 A:ILE210 4.1 9.1 1.0 C17 B:VML404 4.1 12.3 1.0 CG A:TYR111 4.4 8.7 1.0 CD2 A:TYR111 4.5 12.4 1.0 CB A:ILE210 4.5 8.4 1.0 CD2 A:LEU146 4.7 14.1 1.0 C21 B:VML404 4.7 10.5 1.0 F35 B:VML404 4.8 21.6 1.0 C16 B:VML404 4.9 12.0 1.0

Fluorine binding site 2 out of 6 in the NKG2D Complexed with Inhibitor 4A


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 4A within 5.0Å range: probe atom residue distance (Å) B Occ B:F404 b:24.0 occ:1.00 F24 B:VML404 0.0 24.0 1.0 C22 B:VML404 1.4 20.8 1.0 F23 B:VML404 2.1 21.8 1.0 F25 B:VML404 2.2 19.9 1.0 C19 B:VML404 2.3 13.4 1.0 C18 B:VML404 3.1 14.2 1.0 C20 B:VML404 3.3 14.8 1.0 CB A:TYR111 3.5 8.6 1.0 N A:PHE113 3.8 12.6 1.0 N A:GLN112 3.9 12.1 1.0 C A:TYR111 3.9 11.2 1.0 C A:GLN112 3.9 11.7 1.0 CB A:PHE113 4.1 10.9 1.0 CG2 A:ILE210 4.1 9.5 1.0 CA A:GLN112 4.1 9.1 1.0 O A:TYR111 4.1 10.6 1.0 CD1 A:ILE104 4.3 16.3 1.0 CA A:PHE113 4.3 9.8 1.0 C17 B:VML404 4.4 12.3 1.0 CA A:TYR111 4.4 9.6 1.0 C21 B:VML404 4.5 10.5 1.0 O A:GLN112 4.5 12.1 1.0 C1 A:PGE302 4.5 19.0 1.0 O1 A:PGE302 4.5 17.1 1.0 CG A:TYR111 4.6 8.7 1.0 CG1 A:ILE210 4.7 9.1 1.0 C16 B:VML404 4.9 12.0 1.0

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


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 4A within 5.0Å range: probe atom residue distance (Å) B Occ B:F404 b:19.9 occ:1.00 F25 B:VML404 0.0 19.9 1.0 C22 B:VML404 1.3 20.8 1.0 F23 B:VML404 2.1 21.8 1.0 F24 B:VML404 2.2 24.0 1.0 C19 B:VML404 2.3 13.4 1.0 C20 B:VML404 2.8 14.8 1.0 F33 B:VML404 3.2 24.0 1.0 C18 B:VML404 3.6 14.2 1.0 F35 B:VML404 3.6 21.6 1.0 CD1 A:ILE104 3.6 16.3 1.0 C32 B:VML404 3.9 21.8 1.0 CB A:TYR111 4.0 8.6 1.0 C21 B:VML404 4.1 10.5 1.0 CD1 A:LEU145 4.3 11.7 1.0 CG2 A:VAL149 4.6 12.2 1.0 C30 B:VML404 4.6 11.0 1.0 CG A:TYR111 4.6 8.7 1.0 CB A:ILE104 4.7 13.5 1.0 CG2 A:ILE104 4.7 16.8 1.0 C17 B:VML404 4.7 12.3 1.0 CG1 A:ILE104 4.7 15.9 1.0 C16 B:VML404 4.9 12.0 1.0 C29 B:VML404 5.0 11.9 1.0

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


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 4A within 5.0Å range: probe atom residue distance (Å) B Occ B:F404 b:24.0 occ:1.00 F33 B:VML404 0.0 24.0 1.0 C32 B:VML404 1.3 21.8 1.0 F34 B:VML404 2.1 23.7 1.0 F35 B:VML404 2.2 21.6 1.0 C30 B:VML404 2.4 11.0 1.0 C29 B:VML404 2.8 11.9 1.0 F25 B:VML404 3.2 19.9 1.0 CD1 A:LEU145 3.6 11.7 1.0 CD1 A:ILE104 3.6 16.3 1.0 C31 B:VML404 3.6 11.8 1.0 CD1 B:ILE104 3.9 15.9 0.6 C20 B:VML404 4.1 14.8 1.0 CG2 A:ILE104 4.1 16.8 1.0 CD1 B:ILE104 4.1 19.0 0.4 C28 B:VML404 4.2 12.1 1.0 CG1 B:ILE104 4.2 18.4 0.6 C22 B:VML404 4.4 20.8 1.0 CG A:LEU145 4.5 12.4 1.0 CG2 B:ILE104 4.6 20.6 0.6 CG1 A:ILE104 4.7 15.9 1.0 C19 B:VML404 4.7 13.4 1.0 CG1 B:ILE104 4.7 19.9 0.4 C26 B:VML404 4.8 9.8 1.0 CB A:LEU145 4.8 12.0 1.0 CB A:ILE104 4.8 13.5 1.0 CB B:ILE104 4.9 16.9 0.4 C27 B:VML404 5.0 9.7 1.0

Fluorine binding site 5 out of 6 in the NKG2D Complexed with Inhibitor 4A


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 4A within 5.0Å range: probe atom residue distance (Å) B Occ B:F404 b:23.7 occ:1.00 F34 B:VML404 0.0 23.7 1.0 C32 B:VML404 1.4 21.8 1.0 F33 B:VML404 2.1 24.0 1.0 F35 B:VML404 2.2 21.6 1.0 C30 B:VML404 2.4 11.0 1.0 C31 B:VML404 3.2 11.8 1.0 C29 B:VML404 3.2 11.9 1.0 CD1 B:ILE104 3.7 15.9 0.6 CD1 A:LEU148 3.7 24.2 1.0 CG1 B:ILE104 3.7 18.4 0.6 CB A:LEU148 4.1 12.3 1.0 CE2 B:PHE113 4.1 19.2 1.0 CB A:LEU145 4.2 12.0 1.0 CD1 A:LEU145 4.2 11.7 1.0 O A:LEU145 4.2 12.0 1.0 C26 B:VML404 4.4 9.8 1.0 C28 B:VML404 4.4 12.1 1.0 CG A:LEU148 4.6 18.8 1.0 CG A:LEU145 4.6 12.4 1.0 CD1 B:ILE104 4.7 19.0 0.4 CD2 B:PHE113 4.7 18.0 1.0 CA A:LEU145 4.9 10.9 1.0 CB B:ILE104 4.9 16.9 0.4 C27 B:VML404 4.9 9.7 1.0 C A:LEU145 4.9 10.4 1.0 CG2 B:ILE104 5.0 15.0 0.4 CB B:ILE104 5.0 15.4 0.6

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


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 4A within 5.0Å range: probe atom residue distance (Å) B Occ B:F404 b:21.6 occ:1.00 F35 B:VML404 0.0 21.6 1.0 C32 B:VML404 1.3 21.8 1.0 F33 B:VML404 2.2 24.0 1.0 F34 B:VML404 2.2 23.7 1.0 C30 B:VML404 2.4 11.0 1.0 C31 B:VML404 2.7 11.8 1.0 C29 B:VML404 3.6 11.9 1.0 CG2 A:VAL149 3.6 12.2 1.0 F25 B:VML404 3.6 19.9 1.0 O A:LEU145 3.7 12.0 1.0 C20 B:VML404 4.0 14.8 1.0 CD1 A:LEU145 4.1 11.7 1.0 C26 B:VML404 4.1 9.8 1.0 CB A:LEU148 4.2 12.3 1.0 CG A:LEU145 4.3 12.4 1.0 C19 B:VML404 4.4 13.4 1.0 N A:VAL149 4.4 11.0 1.0 C22 B:VML404 4.4 20.8 1.0 C A:LEU148 4.5 13.8 1.0 C A:LEU145 4.5 10.4 1.0 CA A:VAL149 4.5 11.0 1.0 CB A:LEU145 4.5 12.0 1.0 C21 B:VML404 4.6 10.5 1.0 O A:LEU148 4.7 11.2 1.0 CB A:VAL149 4.7 9.9 1.0 O9 B:VML404 4.7 10.8 1.0 C28 B:VML404 4.7 12.1 1.0 F23 B:VML404 4.8 21.8 1.0 C27 B:VML404 4.9 9.7 1.0 CA A:LEU148 4.9 12.1 1.0 CD1 A:LEU148 5.0 24.2 1.0

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