Atomistry » Fluorine » PDB 8rq8-8smc » 8se5
Atomistry »
  Fluorine »
    PDB 8rq8-8smc »
      8se5 »

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: Wed Jul 16 07:21:00 2025

Last articles

Mg in 5EDM
Mg in 5EE3
Mg in 5EDI
Mg in 5EDK
Mg in 5EDH
Mg in 5EDG
Mg in 5EDE
Mg in 5EDD
Mg in 5ED8
Mg in 5ECV
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy