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Fluorine in PDB 8se5: NKG2D Complexed with Inhibitor 14

Protein crystallography data

The structure of NKG2D Complexed with Inhibitor 14, PDB code: 8se5 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) 34.99 / 1.43
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 100.21, 43.361, 64.526, 90, 102.87, 90
R / Rfree (%) 20.6 / 23.1

Fluorine Binding Sites:

The binding sites of Fluorine atom in the NKG2D Complexed with Inhibitor 14 (pdb code 8se5). 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 14, PDB code: 8se5:
Jump to Fluorine binding site number: 1; 2; 3; 4; 5; 6;

Fluorine binding site 1 out of 6 in 8se5

Go back to Fluorine Binding Sites List in 8se5
Fluorine binding site 1 out of 6 in the NKG2D Complexed with Inhibitor 14


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 14 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F303

b:29.2
occ:0.85
 F24 A:ZW7303 0.0 29.2 0.8
C23 A:ZW7303 1.3 28.6 0.8
F25 A:ZW7303 2.1 29.3 0.8
F26 A:ZW7303 2.2 27.4 0.8
C21 A:ZW7303 2.4 20.9 0.8
C20 A:ZW7303 2.8 25.5 0.8
F42 A:ZW7303 3.3 28.3 0.8
CD1 A:LEU145 3.5 21.1 1.0
CD1 A:ILE104 3.5 27.6 1.0
C22 A:ZW7303 3.6 27.0 0.8
CD1 B:ILE104 4.0 29.7 1.0
CG1 B:ILE104 4.0 32.2 1.0
CG2 A:ILE104 4.1 25.8 1.0
C19 A:ZW7303 4.2 27.2 0.8
C37 A:ZW7303 4.2 29.9 0.8
CG A:LEU145 4.3 18.6 1.0
C39 A:ZW7303 4.5 34.2 0.8
CG1 A:ILE104 4.6 23.4 1.0
CG2 B:ILE104 4.6 26.6 1.0
CB A:LEU145 4.6 18.5 1.0
C17 A:ZW7303 4.8 22.0 0.8
C36 A:ZW7303 4.8 23.9 0.8
CB A:ILE104 4.9 22.5 1.0

Fluorine binding site 2 out of 6 in 8se5

Go back to Fluorine Binding Sites List in 8se5
Fluorine binding site 2 out of 6 in the NKG2D Complexed with Inhibitor 14


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 14 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F303

b:29.3
occ:0.85
 F25 A:ZW7303 0.0 29.3 0.8
C23 A:ZW7303 1.3 28.6 0.8
F24 A:ZW7303 2.1 29.2 0.8
F26 A:ZW7303 2.1 27.4 0.8
C21 A:ZW7303 2.3 20.9 0.8
C22 A:ZW7303 3.1 27.0 0.8
C20 A:ZW7303 3.2 25.5 0.8
CG1 B:ILE104 3.8 32.2 1.0
CD1 B:ILE104 3.9 29.7 1.0
CB A:LEU145 4.0 18.5 1.0
CB A:LEU148 4.0 21.1 1.0
CD1 A:LEU148 4.0 34.9 1.0
CD1 A:LEU145 4.1 21.1 1.0
O A:LEU145 4.1 16.2 1.0
C17 A:ZW7303 4.3 22.0 0.8
CG A:LEU145 4.3 18.6 1.0
CE1 B:PHE113 4.4 32.6 0.8
C19 A:ZW7303 4.4 27.2 0.8
CG A:LEU148 4.6 27.5 1.0
CA A:LEU145 4.7 17.3 1.0
C A:LEU145 4.8 16.4 1.0
C18 A:ZW7303 4.9 23.1 0.8
C8 A:ZW7303 4.9 25.4 0.8
F42 A:ZW7303 4.9 28.3 0.8
CD1 B:PHE113 4.9 28.5 0.8

Fluorine binding site 3 out of 6 in 8se5

Go back to Fluorine Binding Sites List in 8se5
Fluorine binding site 3 out of 6 in the NKG2D Complexed with Inhibitor 14


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 14 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F303

b:27.4
occ:0.85
 F26 A:ZW7303 0.0 27.4 0.8
C23 A:ZW7303 1.3 28.6 0.8
F25 A:ZW7303 2.1 29.3 0.8
F24 A:ZW7303 2.2 29.2 0.8
C21 A:ZW7303 2.4 20.9 0.8
C22 A:ZW7303 2.9 27.0 0.8
F42 A:ZW7303 3.4 28.3 0.8
CG2 A:VAL149 3.6 20.1 1.0
C20 A:ZW7303 3.6 25.5 0.8
O A:LEU145 3.7 16.2 1.0
C37 A:ZW7303 3.9 29.9 0.8
CD1 A:LEU145 3.9 21.1 1.0
CG A:LEU145 4.0 18.6 1.0
C39 A:ZW7303 4.2 34.2 0.8
C36 A:ZW7303 4.2 23.9 0.8
C17 A:ZW7303 4.2 22.0 0.8
CB A:LEU145 4.3 18.5 1.0
CB A:LEU148 4.4 21.1 1.0
C A:LEU145 4.4 16.4 1.0
F40 A:ZW7303 4.5 29.3 0.8
N A:VAL149 4.6 17.1 1.0
C38 A:ZW7303 4.6 26.8 0.8
C A:LEU148 4.6 20.5 1.0
CA A:VAL149 4.7 21.4 1.0
C19 A:ZW7303 4.8 27.2 0.8
CB A:VAL149 4.8 17.6 1.0
O A:LEU148 4.9 20.5 1.0
CA A:LEU145 4.9 17.3 1.0

Fluorine binding site 4 out of 6 in 8se5

Go back to Fluorine Binding Sites List in 8se5
Fluorine binding site 4 out of 6 in the NKG2D Complexed with Inhibitor 14


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 14 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F303

b:29.3
occ:0.85
 F40 A:ZW7303 0.0 29.3 0.8
C39 A:ZW7303 1.4 34.2 0.8
F42 A:ZW7303 2.1 28.3 0.8
F41 A:ZW7303 2.2 36.5 0.8
C36 A:ZW7303 2.4 23.9 0.8
C35 A:ZW7303 2.8 18.1 0.8
C37 A:ZW7303 3.6 29.9 0.8
CG2 A:ILE210 3.7 15.9 1.0
CD1 A:ILE210 3.8 19.9 1.0
CG2 A:VAL149 3.9 20.1 1.0
CB A:TYR111 4.0 17.6 1.0
C34 A:ZW7303 4.2 21.7 0.8
CG1 A:ILE210 4.2 18.6 1.0
CG A:TYR111 4.4 17.3 1.0
CD1 A:TYR111 4.5 16.0 1.0
F26 A:ZW7303 4.5 27.4 0.8
CB A:ILE210 4.6 14.5 1.0
C38 A:ZW7303 4.8 26.8 0.8
CD2 A:LEU146 4.8 19.2 1.0
C33 A:ZW7303 5.0 28.7 0.8

Fluorine binding site 5 out of 6 in 8se5

Go back to Fluorine Binding Sites List in 8se5
Fluorine binding site 5 out of 6 in the NKG2D Complexed with Inhibitor 14


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 14 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F303

b:36.5
occ:0.85
 F41 A:ZW7303 0.0 36.5 0.8
C39 A:ZW7303 1.4 34.2 0.8
F42 A:ZW7303 2.1 28.3 0.8
F40 A:ZW7303 2.2 29.3 0.8
C36 A:ZW7303 2.3 23.9 0.8
C35 A:ZW7303 3.1 18.1 0.8
C37 A:ZW7303 3.2 29.9 0.8
CB A:TYR111 3.6 17.6 1.0
N A:PHE113 3.7 17.4 0.8
C A:GLN112 4.0 17.0 1.0
N A:GLN112 4.0 17.6 1.0
C A:TYR111 4.0 18.5 1.0
CB A:PHE113 4.1 18.8 0.8
CA A:GLN112 4.2 17.7 1.0
CD1 A:ILE104 4.2 27.6 1.0
O A:TYR111 4.3 16.5 1.0
CA A:PHE113 4.3 16.2 0.8
C34 A:ZW7303 4.4 21.7 0.8
C38 A:ZW7303 4.4 26.8 0.8
CG2 A:ILE210 4.4 15.9 1.0
CA A:TYR111 4.4 16.8 1.0
O4 A:PGE301 4.5 24.4 1.0
O A:GLN112 4.5 17.6 1.0
CG A:TYR111 4.6 17.3 1.0
C6 A:PGE301 4.7 28.1 1.0
C33 A:ZW7303 4.9 28.7 0.8

Fluorine binding site 6 out of 6 in 8se5

Go back to Fluorine Binding Sites List in 8se5
Fluorine binding site 6 out of 6 in the NKG2D Complexed with Inhibitor 14


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 14 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F303

b:28.3
occ:0.85
 F42 A:ZW7303 0.0 28.3 0.8
C39 A:ZW7303 1.3 34.2 0.8
F41 A:ZW7303 2.1 36.5 0.8
F40 A:ZW7303 2.1 29.3 0.8
C36 A:ZW7303 2.4 23.9 0.8
C37 A:ZW7303 2.8 29.9 0.8
F24 A:ZW7303 3.3 29.2 0.8
F26 A:ZW7303 3.4 27.4 0.8
C35 A:ZW7303 3.6 18.1 0.8
CD1 A:ILE104 3.6 27.6 1.0
C23 A:ZW7303 3.8 28.6 0.8
CB A:TYR111 3.9 17.6 1.0
C38 A:ZW7303 4.2 26.8 0.8
CD1 A:LEU145 4.3 21.1 1.0
C21 A:ZW7303 4.4 20.9 0.8
CG A:TYR111 4.5 17.3 1.0
CG2 A:VAL149 4.6 20.1 1.0
CG2 A:ILE104 4.6 25.8 1.0
CB A:ILE104 4.7 22.5 1.0
C34 A:ZW7303 4.8 21.7 0.8
CG1 A:ILE104 4.8 23.4 1.0
C20 A:ZW7303 4.8 25.5 0.8
F25 A:ZW7303 4.9 29.3 0.8
C33 A:ZW7303 5.0 28.7 0.8
CD2 A:TYR111 5.0 17.7 1.0

Reference:

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
Page generated: Thu Dec 28 04:44:31 2023

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