Fluorine in PDB 8eaa: NKG2D Complexed with Inhibitor 4E

The structure of NKG2D Complexed with Inhibitor 4E, PDB code: 8eaa 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)	32.03 / 1.57
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	100.013, 43.338, 67.109, 90, 106.49, 90
R / Rfree (%)	17.2 / 20.4

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


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 4E within 5.0Å range: probe atom residue distance (Å) B Occ B:F301 b:33.6 occ:0.87 F10 B:VMW301 0.0 33.6 0.9 C8 B:VMW301 1.4 27.9 0.9 F11 B:VMW301 2.1 27.0 0.9 F9 B:VMW301 2.2 32.2 0.9 C6 B:VMW301 2.3 20.3 0.9 CD1 B:ILE104 3.1 23.6 1.0 C5 B:VMW301 3.1 24.0 0.9 C7 B:VMW301 3.2 18.5 0.9 O A:LEU145 3.7 12.5 1.0 CB A:LEU145 3.8 11.6 1.0 CD1 A:LEU145 3.8 12.9 1.0 CD1 A:LEU148 4.0 27.4 1.0 CB A:LEU148 4.0 16.7 1.0 CG A:LEU145 4.0 11.0 1.0 CG1 B:ILE104 4.2 20.2 1.0 C A:LEU145 4.4 11.1 1.0 C4 B:VMW301 4.4 16.8 0.9 CA A:LEU145 4.4 11.4 1.0 C2 B:VMW301 4.4 20.9 0.9 CG A:LEU148 4.5 22.8 1.0 F30 B:VMW301 4.6 28.0 0.9 CE2 B:PHE113 4.6 17.0 0.6 C3 B:VMW301 4.9 20.6 0.9

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


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 4E within 5.0Å range: probe atom residue distance (Å) B Occ B:F301 b:27.0 occ:0.87 F11 B:VMW301 0.0 27.0 0.9 C8 B:VMW301 1.3 27.9 0.9 F10 B:VMW301 2.1 33.6 0.9 F9 B:VMW301 2.2 32.2 0.9 C6 B:VMW301 2.3 20.3 0.9 C5 B:VMW301 2.7 24.0 0.9 CG2 A:VAL149 3.3 17.8 1.0 F30 B:VMW301 3.4 28.0 0.9 O A:LEU145 3.4 12.5 1.0 C7 B:VMW301 3.6 18.5 0.9 C24 B:VMW301 3.6 19.6 0.9 C25 B:VMW301 4.0 13.5 0.9 C28 B:VMW301 4.1 30.5 0.9 C4 B:VMW301 4.1 16.8 0.9 CG A:LEU145 4.1 11.0 1.0 CD1 A:LEU145 4.2 12.9 1.0 N A:VAL149 4.2 13.1 1.0 C A:LEU145 4.3 11.1 1.0 CB A:LEU148 4.3 16.7 1.0 F31 B:VMW301 4.3 30.8 0.9 C23 B:VMW301 4.3 19.0 0.9 CA A:VAL149 4.4 16.0 1.0 C A:LEU148 4.4 12.8 1.0 O15 B:VMW301 4.4 21.9 0.9 CB A:VAL149 4.5 13.0 1.0 CB A:LEU145 4.5 11.6 1.0 C2 B:VMW301 4.7 20.9 0.9 O A:LEU148 4.7 16.2 1.0 CA A:LEU148 4.8 14.0 1.0 C3 B:VMW301 4.9 20.6 0.9 CA A:LEU145 4.9 11.4 1.0 C26 B:VMW301 5.0 13.0 0.9

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


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 4E within 5.0Å range: probe atom residue distance (Å) B Occ B:F301 b:33.3 occ:0.87 F29 B:VMW301 0.0 33.3 0.9 C28 B:VMW301 1.4 30.5 0.9 F30 B:VMW301 2.1 28.0 0.9 F31 B:VMW301 2.2 30.8 0.9 C25 B:VMW301 2.3 13.5 0.9 C26 B:VMW301 3.1 13.0 0.9 C24 B:VMW301 3.3 19.6 0.9 CB A:TYR111 3.4 10.7 1.0 N A:PHE113 3.9 13.9 1.0 N A:GLN112 3.9 11.5 1.0 C A:TYR111 3.9 11.8 1.0 C A:GLN112 4.0 13.2 1.0 CB A:PHE113 4.2 15.7 1.0 CA A:GLN112 4.2 15.0 1.0 CG2 A:ILE210 4.2 14.4 1.0 O A:TYR111 4.3 11.8 1.0 CA A:TYR111 4.3 11.2 1.0 C27 B:VMW301 4.3 17.9 0.9 CA A:PHE113 4.4 13.0 1.0 CD1 A:ILE104 4.4 22.6 1.0 CG A:TYR111 4.4 10.7 1.0 C23 B:VMW301 4.5 19.0 0.9 O A:GLN112 4.6 15.8 1.0 C1 A:PEG302 4.7 20.8 1.0 F9 B:VMW301 4.7 32.2 0.9 O1 A:PEG302 4.7 21.1 1.0 CG1 A:ILE210 4.9 12.7 1.0 C22 B:VMW301 4.9 22.2 0.9 CD1 A:TYR111 4.9 13.0 1.0

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


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 4E within 5.0Å range: probe atom residue distance (Å) B Occ B:F301 b:28.0 occ:0.87 F30 B:VMW301 0.0 28.0 0.9 C28 B:VMW301 1.4 30.5 0.9 F29 B:VMW301 2.1 33.3 0.9 F31 B:VMW301 2.2 30.8 0.9 C25 B:VMW301 2.4 13.5 0.9 F9 B:VMW301 2.6 32.2 0.9 C24 B:VMW301 2.8 19.6 0.9 F11 B:VMW301 3.4 27.0 0.9 C8 B:VMW301 3.5 27.9 0.9 C26 B:VMW301 3.6 13.0 0.9 CD1 A:ILE104 3.8 22.6 1.0 CB A:TYR111 3.9 10.7 1.0 C23 B:VMW301 4.1 19.0 0.9 C6 B:VMW301 4.2 20.3 0.9 CD1 A:LEU145 4.3 12.9 1.0 C7 B:VMW301 4.4 18.5 0.9 CG A:TYR111 4.5 10.7 1.0 F10 B:VMW301 4.6 33.6 0.9 CG2 A:ILE104 4.7 23.4 1.0 CB A:ILE104 4.7 15.3 1.0 C27 B:VMW301 4.8 17.9 0.9 CG2 A:VAL149 4.9 17.8 1.0 CG1 A:ILE104 4.9 16.7 1.0 CD2 A:TYR111 5.0 11.2 1.0 C22 B:VMW301 5.0 22.2 0.9

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


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 4E within 5.0Å range: probe atom residue distance (Å) B Occ B:F301 b:30.8 occ:0.87 F31 B:VMW301 0.0 30.8 0.9 C28 B:VMW301 1.4 30.5 0.9 F29 B:VMW301 2.2 33.3 0.9 F30 B:VMW301 2.2 28.0 0.9 C25 B:VMW301 2.4 13.5 0.9 C26 B:VMW301 2.8 13.0 0.9 C24 B:VMW301 3.6 19.6 0.9 CG2 A:ILE210 3.8 14.4 1.0 CD1 A:ILE210 3.8 14.4 1.0 CB A:TYR111 4.0 10.7 1.0 CG2 A:VAL149 4.0 17.8 1.0 C27 B:VMW301 4.2 17.9 0.9 CG1 A:ILE210 4.2 12.7 1.0 F11 B:VMW301 4.3 27.0 0.9 CG A:TYR111 4.3 10.7 1.0 CD1 A:TYR111 4.3 13.0 1.0 F9 B:VMW301 4.4 32.2 0.9 CD2 A:LEU146 4.5 13.5 1.0 CB A:ILE210 4.6 10.6 1.0 C23 B:VMW301 4.7 19.0 0.9 C8 B:VMW301 5.0 27.9 0.9 C22 B:VMW301 5.0 22.2 0.9

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


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 4E within 5.0Å range: probe atom residue distance (Å) B Occ B:F301 b:32.2 occ:0.87 F9 B:VMW301 0.0 32.2 0.9 C8 B:VMW301 1.4 27.9 0.9 F10 B:VMW301 2.2 33.6 0.9 F11 B:VMW301 2.2 27.0 0.9 C6 B:VMW301 2.4 20.3 0.9 F30 B:VMW301 2.6 28.0 0.9 C7 B:VMW301 2.8 18.5 0.9 CD1 A:LEU145 3.3 12.9 1.0 C5 B:VMW301 3.6 24.0 0.9 C24 B:VMW301 3.6 19.6 0.9 CD1 B:ILE104 3.7 23.6 1.0 C28 B:VMW301 3.8 30.5 0.9 CD1 A:ILE104 4.0 22.6 1.0 CG A:LEU145 4.1 11.0 1.0 C25 B:VMW301 4.1 13.5 0.9 C2 B:VMW301 4.1 20.9 0.9 CG2 A:ILE104 4.4 23.4 1.0 F31 B:VMW301 4.4 30.8 0.9 CG1 B:ILE104 4.5 20.2 1.0 CB A:LEU145 4.6 11.6 1.0 F29 B:VMW301 4.7 33.3 0.9 C23 B:VMW301 4.7 19.0 0.9 C4 B:VMW301 4.8 16.8 0.9 O A:LEU145 5.0 12.5 1.0 C3 B:VMW301 5.0 20.6 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