Fluorine in PDB 5tzy: GPR40 in Complex with Agopam AP8 and Partial Agonist Mk-8666

All present enzymatic activity of GPR40 in Complex with Agopam AP8 and Partial Agonist Mk-8666:
3.2.1.17;

The structure of GPR40 in Complex with Agopam AP8 and Partial Agonist Mk-8666, PDB code: 5tzy was solved by J.Lu, N.Byrne, S.Patel, S.Sharma, S.M.Soisson, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	90.96 / 3.22
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	53.880, 63.950, 90.960, 90.00, 90.52, 90.00
R / Rfree (%)	26.9 / 28.7

The binding sites of Fluorine atom in the GPR40 in Complex with Agopam AP8 and Partial Agonist Mk-8666 (pdb code 5tzy). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 4 binding sites of Fluorine where determined in the GPR40 in Complex with Agopam AP8 and Partial Agonist Mk-8666, PDB code: 5tzy:
Jump to Fluorine binding site number: 1; 2; 3; 4;

Fluorine binding site 1 out of 4 in the GPR40 in Complex with Agopam AP8 and Partial Agonist Mk-8666


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of GPR40 in Complex with Agopam AP8 and Partial Agonist Mk-8666 within 5.0Å range: probe atom residue distance (Å) B Occ A:F2403 b:0.1 occ:1.00 F3 A:7OS2403 0.0 0.1 1.0 C28 A:7OS2403 1.3 0.5 1.0 F2 A:7OS2403 2.1 0.5 1.0 F1 A:7OS2403 2.2 0.0 1.0 O3 A:7OS2403 2.2 99.2 1.0 C23 A:7OS2403 2.7 0.4 1.0 CD2 A:LEU133 3.3 95.3 1.0 CG2 A:VAL134 3.3 81.7 1.0 CD2 A:LEU190 3.3 0.6 1.0 C24 A:7OS2403 3.3 0.1 1.0 C22 A:7OS2403 3.4 0.4 1.0 CG A:LEU133 3.7 98.9 1.0 C21 A:7OS2403 3.7 99.0 1.0 C29 A:7OS2403 3.8 0.7 1.0 CB A:LEU133 4.2 95.5 1.0 C25 A:7OS2403 4.4 0.3 1.0 C27 A:7OS2403 4.4 0.6 1.0 CG A:LEU190 4.5 0.0 1.0 O A:ILE130 4.6 91.0 1.0 N A:VAL134 4.6 87.1 1.0 CB A:LEU190 4.6 0.9 1.0 CB A:VAL134 4.7 83.0 1.0 CG2 A:ILE130 4.7 79.2 1.0 C26 A:7OS2403 4.8 0.6 1.0 CA A:LEU190 4.9 0.1 1.0 CA A:ILE130 5.0 83.8 1.0

Fluorine binding site 2 out of 4 in the GPR40 in Complex with Agopam AP8 and Partial Agonist Mk-8666


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of GPR40 in Complex with Agopam AP8 and Partial Agonist Mk-8666 within 5.0Å range: probe atom residue distance (Å) B Occ A:F2403 b:0.0 occ:1.00 F1 A:7OS2403 0.0 0.0 1.0 C28 A:7OS2403 1.3 0.5 1.0 F2 A:7OS2403 2.1 0.5 1.0 F3 A:7OS2403 2.2 0.1 1.0 O3 A:7OS2403 2.2 99.2 1.0 CA A:GLY95 3.1 92.6 1.0 C21 A:7OS2403 3.2 99.0 1.0 CG2 A:ILE130 3.3 79.2 1.0 C23 A:7OS2403 3.3 0.4 1.0 C29 A:7OS2403 3.5 0.7 1.0 CG1 A:ILE130 3.5 79.8 1.0 C22 A:7OS2403 3.7 0.4 1.0 N A:GLY95 3.8 92.3 1.0 CB A:ILE130 3.8 80.2 1.0 O A:ALA92 4.2 96.7 1.0 CG2 A:VAL134 4.2 81.7 1.0 CA A:ILE130 4.2 83.8 1.0 C A:GLY95 4.3 92.0 1.0 N A:7OS2403 4.3 94.5 1.0 C24 A:7OS2403 4.4 0.1 1.0 CD1 A:ILE130 4.4 78.5 1.0 C19 A:7OS2403 4.5 94.5 1.0 O A:ILE130 4.6 91.0 1.0 C A:ILE130 4.8 87.2 1.0 O A:GLY95 4.8 93.3 1.0 CD2 A:LEU133 4.9 95.3 1.0 C18 A:7OS2403 4.9 93.3 1.0 O A:TYR91 4.9 0.0 1.0 CA A:ALA92 5.0 0.5 1.0

Fluorine binding site 3 out of 4 in the GPR40 in Complex with Agopam AP8 and Partial Agonist Mk-8666


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of GPR40 in Complex with Agopam AP8 and Partial Agonist Mk-8666 within 5.0Å range: probe atom residue distance (Å) B Occ A:F2403 b:0.5 occ:1.00 F2 A:7OS2403 0.0 0.5 1.0 C28 A:7OS2403 1.3 0.5 1.0 F3 A:7OS2403 2.1 0.1 1.0 F1 A:7OS2403 2.1 0.0 1.0 O3 A:7OS2403 2.2 99.2 1.0 O A:TYR91 3.2 0.0 1.0 C23 A:7OS2403 3.4 0.4 1.0 CG2 A:VAL134 3.5 81.7 1.0 N A:GLY95 3.7 92.3 1.0 O A:LEU190 3.9 97.5 1.0 C24 A:7OS2403 3.9 0.1 1.0 O A:ALA92 3.9 96.7 1.0 CA A:GLY95 3.9 92.6 1.0 C A:TYR91 3.9 0.0 1.0 CA A:ALA92 4.2 0.5 1.0 CD2 A:LEU190 4.3 0.6 1.0 N A:ALA92 4.4 0.6 1.0 CB A:LEU190 4.4 0.9 1.0 C22 A:7OS2403 4.4 0.4 1.0 C A:ALA92 4.4 98.3 1.0 CG A:PRO194 4.5 85.6 1.0 C21 A:7OS2403 4.7 99.0 1.0 CA A:LEU190 4.7 0.1 1.0 C A:LEU190 4.7 1.0 1.0 CG2 A:ILE130 4.7 79.2 1.0 C A:GLY94 4.7 98.2 1.0 CG A:LEU190 4.9 0.0 1.0 CB A:VAL134 5.0 83.0 1.0

Fluorine binding site 4 out of 4 in the GPR40 in Complex with Agopam AP8 and Partial Agonist Mk-8666


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 4 of GPR40 in Complex with Agopam AP8 and Partial Agonist Mk-8666 within 5.0Å range: probe atom residue distance (Å) B Occ A:F2403 b:0.5 occ:1.00 F A:7OS2403 0.0 0.5 1.0 C26 A:7OS2403 1.4 0.6 1.0 C25 A:7OS2403 2.3 0.3 1.0 C27 A:7OS2403 2.4 0.6 1.0 CD2 A:LEU193 3.5 0.2 1.0 C24 A:7OS2403 3.6 0.1 1.0 C22 A:7OS2403 3.6 0.4 1.0 C23 A:7OS2403 4.1 0.4 1.0 CG A:LEU193 4.3 0.7 1.0 O A:LEU189 4.5 0.1 1.0 CB A:LEU193 4.6 0.9 1.0 CD2 A:LEU133 4.6 95.3 1.0 C21 A:7OS2403 4.9 99.0 1.0

J.Lu, N.Byrne, J.Wang, G.Bricogne, F.K.Brown, H.R.Chobanian, S.L.Colletti, J.Di Salvo, B.Thomas-Fowlkes, Y.Guo, D.L.Hall, J.Hadix, N.B.Hastings, J.D.Hermes, T.Ho, A.D.Howard, H.Josien, M.Kornienko, K.J.Lumb, M.W.Miller, S.B.Patel, B.Pio, C.W.Plummer, B.S.Sherborne, P.Sheth, S.Souza, S.Tummala, C.Vonrhein, M.Webb, S.J.Allen, J.M.Johnston, A.B.Weinglass, S.Sharma, S.M.Soisson. Structural Basis For the Cooperative Allosteric Activation of the Free Fatty Acid Receptor GPR40. Nat. Struct. Mol. Biol. V. 24 570 2017.
ISSN: ESSN 1545-9985
PubMed: 28581512
DOI: 10.1038/NSMB.3417