Fluorine in PDB 8se6: NKG2D Complexed with Inhibitor 36

The structure of NKG2D Complexed with Inhibitor 36, PDB code: 8se6 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)	43.44 / 1.36
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	100.041, 43.483, 64.188, 90, 102.87, 90
R / Rfree (%)	19.4 / 21.1

The binding sites of Fluorine atom in the NKG2D Complexed with Inhibitor 36 (pdb code 8se6). 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 36, PDB code: 8se6:
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 36


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 36 within 5.0Å range: probe atom residue distance (Å) B Occ B:F301 b:27.3 occ:0.86 F23 B:ZWA301 0.0 27.3 0.9 C22 B:ZWA301 1.4 30.3 0.9 F24 B:ZWA301 2.2 31.1 0.9 F25 B:ZWA301 2.2 26.5 0.9 C19 B:ZWA301 2.4 22.6 0.9 C18 B:ZWA301 2.9 17.6 0.9 C20 B:ZWA301 3.5 20.0 0.9 CD1 B:ILE210 3.7 16.7 1.0 CG2 B:VAL149 3.8 18.2 1.0 CG2 B:ILE210 3.9 14.7 1.0 C35 B:ZWA301 4.1 21.4 0.9 F38 B:ZWA301 4.1 25.5 0.9 CB B:TYR111 4.2 16.6 1.0 CG1 B:ILE210 4.2 16.8 1.0 C17 B:ZWA301 4.2 18.0 0.9 C36 B:ZWA301 4.5 22.4 0.9 CG B:TYR111 4.5 14.4 1.0 F37 B:ZWA301 4.6 23.7 0.9 CD1 B:TYR111 4.6 15.8 1.0 CD2 B:LEU146 4.7 16.7 1.0 C21 B:ZWA301 4.7 19.1 0.9 CB B:ILE210 4.7 14.3 1.0 C16 B:ZWA301 5.0 18.4 0.9 CG1 B:VAL149 5.0 19.3 1.0

Fluorine binding site 2 out of 6 in the NKG2D Complexed with Inhibitor 36


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 36 within 5.0Å range: probe atom residue distance (Å) B Occ B:F301 b:31.1 occ:0.86 F24 B:ZWA301 0.0 31.1 0.9 C22 B:ZWA301 1.4 30.3 0.9 F23 B:ZWA301 2.2 27.3 0.9 F25 B:ZWA301 2.2 26.5 0.9 C19 B:ZWA301 2.4 22.6 0.9 C18 B:ZWA301 3.0 17.6 0.9 C20 B:ZWA301 3.4 20.0 0.9 CB B:TYR111 3.6 16.6 1.0 N B:PHE113 3.7 18.1 1.0 C B:GLN112 3.8 14.6 1.0 CG2 B:ILE210 3.9 14.7 1.0 N B:GLN112 3.9 16.2 1.0 CB B:PHE113 4.0 17.9 1.0 C B:TYR111 4.1 18.1 1.0 CA B:GLN112 4.1 15.9 1.0 CA B:PHE113 4.2 16.4 1.0 O B:GLN112 4.2 15.8 1.0 C17 B:ZWA301 4.3 18.0 0.9 CG1 B:ILE210 4.4 16.8 1.0 O B:TYR111 4.4 16.6 1.0 CA B:TYR111 4.4 17.7 1.0 C21 B:ZWA301 4.6 19.1 0.9 CD1 B:ILE210 4.6 16.7 1.0 CG B:TYR111 4.6 14.4 1.0 CD1 B:ILE104 4.6 24.7 1.0 CB B:ILE210 4.7 14.3 1.0 C16 B:ZWA301 5.0 18.4 0.9

Fluorine binding site 3 out of 6 in the NKG2D Complexed with Inhibitor 36


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 36 within 5.0Å range: probe atom residue distance (Å) B Occ B:F301 b:26.5 occ:0.86 F25 B:ZWA301 0.0 26.5 0.9 C22 B:ZWA301 1.4 30.3 0.9 F24 B:ZWA301 2.2 31.1 0.9 F23 B:ZWA301 2.2 27.3 0.9 C19 B:ZWA301 2.4 22.6 0.9 C20 B:ZWA301 2.8 20.0 0.9 CD1 B:ILE104 3.5 24.7 1.0 F37 B:ZWA301 3.5 23.7 0.9 C35 B:ZWA301 3.6 21.4 0.9 C18 B:ZWA301 3.7 17.6 0.9 C40 B:ZWA301 3.8 22.2 0.9 CB B:TYR111 3.9 16.6 1.0 C36 B:ZWA301 4.0 22.4 0.9 N32 B:ZWA301 4.1 28.8 0.9 C21 B:ZWA301 4.2 19.1 0.9 C34 B:ZWA301 4.2 21.5 0.9 F38 B:ZWA301 4.2 25.5 0.9 C33 B:ZWA301 4.6 23.4 0.9 CG B:TYR111 4.6 14.4 1.0 C30 B:ZWA301 4.6 21.7 0.9 CB B:ILE104 4.6 19.8 1.0 CG1 B:ILE104 4.7 20.5 1.0 CG2 B:ILE104 4.7 22.0 1.0 C29 B:ZWA301 4.8 24.1 0.9 C17 B:ZWA301 4.8 18.0 0.9 CG2 B:VAL149 4.9 18.2 1.0

Fluorine binding site 4 out of 6 in the NKG2D Complexed with Inhibitor 36


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 36 within 5.0Å range: probe atom residue distance (Å) B Occ B:F301 b:23.7 occ:0.86 F37 B:ZWA301 0.0 23.7 0.9 C36 B:ZWA301 1.3 22.4 0.9 F38 B:ZWA301 2.2 25.5 0.9 F39 B:ZWA301 2.2 25.4 0.9 C35 B:ZWA301 2.3 21.4 0.9 C34 B:ZWA301 2.9 21.5 0.9 C40 B:ZWA301 3.1 22.2 0.9 CD2 B:TYR111 3.3 16.5 1.0 CG2 B:ILE104 3.5 22.0 1.0 F25 B:ZWA301 3.5 26.5 0.9 CE2 B:TYR111 3.8 15.2 1.0 CG B:TYR111 3.9 14.4 1.0 CB B:TYR106 4.1 15.3 1.0 CB B:TYR111 4.2 16.6 1.0 C33 B:ZWA301 4.3 23.4 0.9 N32 B:ZWA301 4.3 28.8 0.9 CB B:ILE104 4.5 19.8 1.0 F23 B:ZWA301 4.6 27.3 0.9 CG2 A:ILE104 4.6 18.1 1.0 C22 B:ZWA301 4.6 30.3 0.9 CZ B:TYR111 4.7 14.4 1.0 CD1 B:TYR111 4.7 15.8 1.0 CD1 B:ILE104 4.8 24.7 1.0 CG B:TYR106 4.8 16.5 1.0

Fluorine binding site 5 out of 6 in the NKG2D Complexed with Inhibitor 36


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 36 within 5.0Å range: probe atom residue distance (Å) B Occ B:F301 b:25.5 occ:0.86 F38 B:ZWA301 0.0 25.5 0.9 C36 B:ZWA301 1.4 22.4 0.9 F37 B:ZWA301 2.2 23.7 0.9 F39 B:ZWA301 2.2 25.4 0.9 C35 B:ZWA301 2.3 21.4 0.9 CE2 B:TYR111 3.3 15.2 1.0 CD2 B:TYR111 3.3 16.5 1.0 CZ B:TYR111 3.5 14.4 1.0 CD2 B:LEU146 3.5 16.7 1.0 CG B:TYR111 3.6 14.4 1.0 C34 B:ZWA301 3.7 21.5 0.9 CE1 B:TYR111 3.7 15.1 1.0 CD1 B:TYR111 3.8 15.8 1.0 F23 B:ZWA301 4.1 27.3 0.9 OH B:TYR111 4.2 16.1 1.0 CG B:LEU146 4.2 16.5 1.0 F25 B:ZWA301 4.2 26.5 0.9 CB B:TYR111 4.4 16.6 1.0 C40 B:ZWA301 4.6 22.2 0.9 N B:LEU146 4.6 15.5 1.0 C33 B:ZWA301 4.8 23.4 0.9 C22 B:ZWA301 4.8 30.3 0.9 CA B:LEU146 4.8 16.3 1.0 C B:LEU145 4.9 17.1 1.0 CB B:TYR106 4.9 15.3 1.0

Fluorine binding site 6 out of 6 in the NKG2D Complexed with Inhibitor 36


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 36 within 5.0Å range: probe atom residue distance (Å) B Occ B:F301 b:25.4 occ:0.86 F39 B:ZWA301 0.0 25.4 0.9 C36 B:ZWA301 1.3 22.4 0.9 F37 B:ZWA301 2.2 23.7 0.9 F38 B:ZWA301 2.2 25.5 0.9 C35 B:ZWA301 2.3 21.4 0.9 C34 B:ZWA301 2.8 21.5 0.9 CD2 B:TYR106 3.5 16.0 1.0 CG B:TYR106 3.6 16.5 1.0 CB B:TYR106 3.6 15.3 1.0 CB B:LEU145 3.7 25.2 1.0 C40 B:ZWA301 3.8 22.2 0.9 C B:LEU145 4.1 17.1 1.0 C33 B:ZWA301 4.2 23.4 0.9 CA B:LEU145 4.3 20.3 1.0 CE2 B:TYR111 4.3 15.2 1.0 N B:LEU146 4.3 15.5 1.0 CE2 B:TYR106 4.3 18.7 1.0 CG2 A:ILE104 4.3 18.1 1.0 O B:LEU145 4.4 17.3 1.0 CD1 B:TYR106 4.5 22.0 1.0 CD2 B:TYR111 4.5 16.5 1.0 N B:LEU145 4.6 15.9 1.0 CG B:LEU145 4.8 25.5 1.0 N32 B:ZWA301 4.8 28.8 0.9 CZ B:TYR111 4.9 14.4 1.0 CD1 B:LEU145 4.9 22.7 1.0

J.Wang, K.M.Nakafuku, J.Ziff, C.F.Gelin, H.Gholami, A.A.Thompson, N.K.Karpowich, L.Limon, H.R.Coate, K.L.Damm-Ganamet, A.Y.Shih, J.C.Grant, M.Cote, P.A.Mak, H.A.Pascual, M.L.Rives, J.P.Edwards, J.D.Venable, H.Venkatesan, Z.Shi, S.J.Allen, S.Sharma, P.P.Kung, B.T.Shireman. Development of Small Molecule Inhibitors of Natural Killer Group 2D Receptor (NKG2D). Bioorg.Med.Chem.Lett. 29492 2023.
ISSN: ESSN 1464-3405
PubMed: 37778428
DOI: 10.1016/J.BMCL.2023.129492