Fluorine in PDB 8ea9: NKG2D Complexed with Inhibitor 4D

The structure of NKG2D Complexed with Inhibitor 4D, PDB code: 8ea9 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)	32.28 / 1.58
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	99.719, 43.4, 64.777, 90, 102.83, 90
R / Rfree (%)	18 / 21.2

The binding sites of Fluorine atom in the NKG2D Complexed with Inhibitor 4D (pdb code 8ea9). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 9 binding sites of Fluorine where determined in the NKG2D Complexed with Inhibitor 4D, PDB code: 8ea9:
Jump to Fluorine binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9;

Fluorine binding site 1 out of 9 in the NKG2D Complexed with Inhibitor 4D


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 4D within 5.0Å range: probe atom residue distance (Å) B Occ B:F302 b:32.8 occ:0.93 F23 B:VMQ302 0.0 32.8 0.9 C22 B:VMQ302 1.4 39.0 0.9 F25 B:VMQ302 2.2 33.0 0.9 F24 B:VMQ302 2.2 45.5 0.9 C19 B:VMQ302 2.4 22.6 0.9 C18 B:VMQ302 2.9 17.6 0.9 C20 B:VMQ302 3.6 31.9 0.9 CG2 A:ILE210 3.7 17.8 1.0 CD1 A:ILE210 3.8 20.5 1.0 CB A:TYR111 3.8 14.6 1.0 CG1 A:ILE210 4.2 18.1 1.0 F38 B:VMQ302 4.2 33.2 0.9 C17 B:VMQ302 4.2 26.5 0.9 CG A:TYR111 4.3 14.3 1.0 CG2 A:VAL149 4.3 22.3 1.0 CD1 A:TYR111 4.4 16.4 1.0 CB A:ILE210 4.6 15.3 1.0 F37 B:VMQ302 4.6 27.9 0.9 C21 B:VMQ302 4.7 30.9 0.9 CD2 A:LEU146 4.8 17.8 1.0

Fluorine binding site 2 out of 9 in the NKG2D Complexed with Inhibitor 4D


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 4D within 5.0Å range: probe atom residue distance (Å) B Occ B:F302 b:45.5 occ:0.93 F24 B:VMQ302 0.0 45.5 0.9 C22 B:VMQ302 1.4 39.0 0.9 F25 B:VMQ302 2.2 33.0 0.9 F23 B:VMQ302 2.2 32.8 0.9 C19 B:VMQ302 2.3 22.6 0.9 C18 B:VMQ302 3.2 17.6 0.9 C20 B:VMQ302 3.2 31.9 0.9 CB A:TYR111 3.4 14.6 1.0 N A:PHE113 3.7 18.7 1.0 C A:TYR111 3.9 16.9 1.0 N A:GLN112 3.9 17.6 1.0 C A:GLN112 3.9 18.4 1.0 CA A:GLN112 4.1 18.4 1.0 CB A:PHE113 4.1 19.2 1.0 O A:TYR111 4.1 17.2 1.0 CA A:PHE113 4.3 17.5 1.0 CA A:TYR111 4.3 15.8 1.0 CD1 A:ILE104 4.3 24.2 1.0 CG2 A:ILE210 4.3 17.8 1.0 C17 B:VMQ302 4.4 26.5 0.9 C21 B:VMQ302 4.4 30.9 0.9 O4 A:PEG302 4.4 21.7 1.0 O A:GLN112 4.5 18.3 1.0 C4 A:PEG302 4.5 24.2 1.0 CG A:TYR111 4.6 14.3 1.0 F38 B:VMQ302 4.7 33.2 0.9 C16 B:VMQ302 4.9 23.6 0.9 CG1 A:ILE210 5.0 18.1 1.0

Fluorine binding site 3 out of 9 in the NKG2D Complexed with Inhibitor 4D


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 4D within 5.0Å range: probe atom residue distance (Å) B Occ B:F302 b:33.0 occ:0.93 F25 B:VMQ302 0.0 33.0 0.9 C22 B:VMQ302 1.4 39.0 0.9 F24 B:VMQ302 2.2 45.5 0.9 F23 B:VMQ302 2.2 32.8 0.9 C19 B:VMQ302 2.4 22.6 0.9 F38 B:VMQ302 2.5 33.2 0.9 C20 B:VMQ302 2.7 31.9 0.9 C36 B:VMQ302 3.6 25.2 0.9 C18 B:VMQ302 3.6 17.6 0.9 CD1 A:ILE104 3.7 24.2 1.0 F37 B:VMQ302 3.8 27.9 0.9 CB A:TYR111 3.9 14.6 1.0 C21 B:VMQ302 4.1 30.9 0.9 C28 B:VMQ302 4.2 22.4 0.9 C29 B:VMQ302 4.3 23.1 0.9 CD1 A:LEU145 4.4 20.5 1.0 CG A:TYR111 4.5 14.3 1.0 CG2 A:ILE104 4.7 27.5 1.0 F39 B:VMQ302 4.7 28.1 0.9 CB A:ILE104 4.7 22.7 1.0 C17 B:VMQ302 4.8 26.5 0.9 CG1 A:ILE104 4.8 20.0 1.0 C16 B:VMQ302 4.9 23.6 0.9 CD2 A:TYR111 5.0 16.4 1.0

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


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 4D within 5.0Å range: probe atom residue distance (Å) B Occ B:F302 b:28.6 occ:0.93 F33 B:VMQ302 0.0 28.6 0.9 C32 B:VMQ302 1.3 27.1 0.9 F35 B:VMQ302 2.1 31.2 0.9 F34 B:VMQ302 2.2 38.2 0.9 C30 B:VMQ302 2.4 23.2 0.9 C31 B:VMQ302 2.8 27.1 0.9 CG2 B:VAL149 3.1 22.3 1.0 O B:LEU145 3.1 17.4 1.0 N B:VAL149 3.6 18.8 1.0 C29 B:VMQ302 3.6 23.1 0.9 C B:LEU148 3.7 20.4 1.0 CB B:LEU148 3.8 21.4 1.0 CA B:VAL149 3.9 19.4 1.0 O B:LEU148 3.9 22.4 1.0 C B:LEU145 4.1 18.8 1.0 CB B:VAL149 4.1 19.4 1.0 C26 B:VMQ302 4.2 24.5 0.9 CA B:LEU148 4.2 20.0 1.0 CG B:LEU145 4.4 15.5 1.0 CZ B:PHE113 4.4 12.3 0.5 N B:LEU148 4.5 20.3 1.0 CD1 B:LEU145 4.6 18.2 1.0 CB B:LEU145 4.6 17.7 1.0 C28 B:VMQ302 4.8 22.4 0.9 CA B:LEU146 4.8 16.2 1.0 N B:LEU146 4.8 19.0 1.0 CA B:LEU145 4.9 17.2 1.0 O5 B:VMQ302 5.0 25.5 0.9 CG B:LEU148 5.0 24.9 1.0 C27 B:VMQ302 5.0 33.5 0.9

Fluorine binding site 5 out of 9 in the NKG2D Complexed with Inhibitor 4D


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 4D within 5.0Å range: probe atom residue distance (Å) B Occ B:F302 b:38.2 occ:0.93 F34 B:VMQ302 0.0 38.2 0.9 C32 B:VMQ302 1.4 27.1 0.9 F33 B:VMQ302 2.2 28.6 0.9 F35 B:VMQ302 2.2 31.2 0.9 C30 B:VMQ302 2.4 23.2 0.9 C29 B:VMQ302 3.0 23.1 0.9 CD1 B:ILE104 3.3 21.9 0.4 CD1 B:LEU145 3.4 18.2 1.0 C31 B:VMQ302 3.5 27.1 0.9 CZ B:PHE113 3.7 12.3 0.5 CG B:LEU145 3.9 15.5 1.0 CE2 B:PHE113 4.1 23.2 0.5 CD1 A:ILE104 4.2 24.2 1.0 C28 B:VMQ302 4.3 22.4 0.9 CG2 B:VAL149 4.3 22.3 1.0 CB B:LEU145 4.5 17.7 1.0 O B:LEU145 4.5 17.4 1.0 CD1 B:ILE104 4.6 26.6 0.6 C26 B:VMQ302 4.6 24.5 0.9 CG1 B:ILE104 4.8 17.4 0.4 CE1 B:PHE113 4.9 12.4 0.5 CG2 B:ILE104 4.9 23.2 0.6 C27 B:VMQ302 5.0 33.5 0.9

Fluorine binding site 6 out of 9 in the NKG2D Complexed with Inhibitor 4D


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 4D within 5.0Å range: probe atom residue distance (Å) B Occ B:F302 b:31.2 occ:0.93 F35 B:VMQ302 0.0 31.2 0.9 C32 B:VMQ302 1.4 27.1 0.9 F33 B:VMQ302 2.1 28.6 0.9 F34 B:VMQ302 2.2 38.2 0.9 C30 B:VMQ302 2.4 23.2 0.9 C29 B:VMQ302 3.0 23.1 0.9 CD1 A:ILE104 3.3 24.2 1.0 C31 B:VMQ302 3.5 27.1 0.9 O B:LEU145 3.7 17.4 1.0 CB B:LEU145 3.9 17.7 1.0 CD1 B:LEU145 4.0 18.2 1.0 CB B:LEU148 4.0 21.4 1.0 CG B:LEU145 4.2 15.5 1.0 C20 B:VMQ302 4.2 31.9 0.9 C21 B:VMQ302 4.2 30.9 0.9 C28 B:VMQ302 4.3 22.4 0.9 CD1 B:LEU148 4.3 29.6 1.0 CG1 A:ILE104 4.4 20.0 1.0 C B:LEU145 4.5 18.8 1.0 CA B:LEU145 4.6 17.2 1.0 C26 B:VMQ302 4.6 24.5 0.9 CG B:LEU148 4.7 24.9 1.0 CD1 B:ILE104 4.9 21.9 0.4 C27 B:VMQ302 4.9 33.5 0.9

Fluorine binding site 7 out of 9 in the NKG2D Complexed with Inhibitor 4D


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 4D within 5.0Å range: probe atom residue distance (Å) B Occ B:F302 b:27.9 occ:0.93 F37 B:VMQ302 0.0 27.9 0.9 C36 B:VMQ302 1.4 25.2 0.9 F38 B:VMQ302 2.2 33.2 0.9 F39 B:VMQ302 2.2 28.1 0.9 C28 B:VMQ302 2.4 22.4 0.9 C27 B:VMQ302 2.7 33.5 0.9 O A:LEU145 3.2 18.3 1.0 CG2 A:VAL149 3.2 22.3 1.0 C29 B:VMQ302 3.6 23.1 0.9 N A:VAL149 3.8 19.9 1.0 F25 B:VMQ302 3.8 33.0 0.9 C A:LEU148 3.9 20.5 1.0 CB A:LEU148 4.0 21.1 1.0 CA A:VAL149 4.0 22.1 1.0 C20 B:VMQ302 4.1 31.9 0.9 C A:LEU145 4.1 16.5 1.0 C26 B:VMQ302 4.1 24.5 0.9 CB A:VAL149 4.2 19.1 1.0 O A:LEU148 4.3 20.7 1.0 O9 B:VMQ302 4.3 28.5 0.9 CG A:LEU145 4.3 16.3 1.0 C19 B:VMQ302 4.4 22.6 0.9 CA A:LEU148 4.4 19.1 1.0 C22 B:VMQ302 4.5 39.0 0.9 CD1 A:LEU145 4.5 20.5 1.0 CB A:LEU145 4.6 17.2 1.0 C21 B:VMQ302 4.6 30.9 0.9 F23 B:VMQ302 4.6 32.8 0.9 N A:LEU148 4.7 20.1 1.0 C30 B:VMQ302 4.7 23.2 0.9 CA A:LEU146 4.8 15.3 1.0 N A:LEU146 4.8 15.8 1.0 CA A:LEU145 4.9 17.3 1.0 C31 B:VMQ302 4.9 27.1 0.9 C6 B:VMQ302 4.9 20.9 0.9

Fluorine binding site 8 out of 9 in the NKG2D Complexed with Inhibitor 4D


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 4D within 5.0Å range: probe atom residue distance (Å) B Occ B:F302 b:33.2 occ:0.93 F38 B:VMQ302 0.0 33.2 0.9 C36 B:VMQ302 1.4 25.2 0.9 F37 B:VMQ302 2.2 27.9 0.9 F39 B:VMQ302 2.2 28.1 0.9 C28 B:VMQ302 2.4 22.4 0.9 F25 B:VMQ302 2.5 33.0 0.9 C29 B:VMQ302 2.8 23.1 0.9 CD1 A:LEU145 3.4 20.5 1.0 C27 B:VMQ302 3.6 33.5 0.9 C20 B:VMQ302 3.6 31.9 0.9 C22 B:VMQ302 3.7 39.0 0.9 CG A:LEU145 3.9 16.3 1.0 CD1 B:ILE104 4.0 26.6 0.6 C19 B:VMQ302 4.0 22.6 0.9 CD1 A:ILE104 4.2 24.2 1.0 F23 B:VMQ302 4.2 32.8 0.9 C30 B:VMQ302 4.2 23.2 0.9 CB A:LEU145 4.4 17.2 1.0 O A:LEU145 4.5 18.3 1.0 C21 B:VMQ302 4.6 30.9 0.9 F24 B:VMQ302 4.7 45.5 0.9 CG1 B:ILE104 4.7 20.8 0.6 C26 B:VMQ302 4.7 24.5 0.9 CG2 A:ILE104 4.8 27.5 1.0 CG2 A:VAL149 4.8 22.3 1.0 CG2 B:ILE104 4.8 21.7 0.4 C31 B:VMQ302 5.0 27.1 0.9

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


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 4D within 5.0Å range: probe atom residue distance (Å) B Occ B:F302 b:28.1 occ:0.93 F39 B:VMQ302 0.0 28.1 0.9 C36 B:VMQ302 1.3 25.2 0.9 F37 B:VMQ302 2.2 27.9 0.9 F38 B:VMQ302 2.2 33.2 0.9 C28 B:VMQ302 2.3 22.4 0.9 C27 B:VMQ302 3.1 33.5 0.9 C29 B:VMQ302 3.1 23.1 0.9 CD1 B:ILE104 3.2 26.6 0.6 O A:LEU145 3.5 18.3 1.0 CB A:LEU145 3.8 17.2 1.0 CB A:LEU148 3.8 21.1 1.0 CD1 A:LEU145 4.0 20.5 1.0 CG A:LEU145 4.0 16.3 1.0 CD1 A:LEU148 4.1 30.6 1.0 C A:LEU145 4.2 16.5 1.0 CG1 B:ILE104 4.3 20.8 0.6 CG2 B:ILE104 4.3 21.7 0.4 C26 B:VMQ302 4.3 24.5 0.9 C30 B:VMQ302 4.4 23.2 0.9 CA A:LEU145 4.4 17.3 1.0 CG A:LEU148 4.5 24.2 1.0 CE2 B:PHE113 4.7 23.2 0.5 F25 B:VMQ302 4.7 33.0 0.9 C31 B:VMQ302 4.8 27.1 0.9 CA A:LEU148 4.9 19.1 1.0 C3 A:PEG301 5.0 31.8 1.0 C A:LEU148 5.0 20.5 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