Fluorine in PDB 5v57: 3.0A Syn Structure of the Multi-Domain Human Smoothened Receptor in Complex with TC114

The structure of 3.0A Syn Structure of the Multi-Domain Human Smoothened Receptor in Complex with TC114, PDB code: 5v57 was solved by X.Zhang, F.Zhao, Y.Wu, J.Yang, G.W.Han, S.Zhao, A.Ishchenko, L.Ye, X.Lin, K.Ding, V.Dharmarajan, P.R.Griffin, C.Gati, G.Nelson, M.S.Hunter, M.A.Hanson, V.Cherezov, R.C.Stevens, W.Tan, H.Tao, F.Xu, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	48.38 / 3.00
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	40.080, 356.360, 59.090, 90.00, 102.79, 90.00
R / Rfree (%)	20.3 / 24

The binding sites of Fluorine atom in the 3.0A Syn Structure of the Multi-Domain Human Smoothened Receptor in Complex with TC114 (pdb code 5v57). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 6 binding sites of Fluorine where determined in the 3.0A Syn Structure of the Multi-Domain Human Smoothened Receptor in Complex with TC114, PDB code: 5v57:
Jump to Fluorine binding site number: 1; 2; 3; 4; 5; 6;

Fluorine binding site 1 out of 6 in the 3.0A Syn Structure of the Multi-Domain Human Smoothened Receptor in Complex with TC114


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of 3.0A Syn Structure of the Multi-Domain Human Smoothened Receptor in Complex with TC114 within 5.0Å range: probe atom residue distance (Å) B Occ A:F1201 b:91.2 occ:1.00 F2 A:8361201 0.0 91.2 1.0 C4 A:8361201 1.4 91.4 1.0 F3 A:8361201 2.2 91.9 1.0 F4 A:8361201 2.2 91.9 1.0 C3 A:8361201 2.4 91.4 1.0 C5 A:8361201 3.1 89.2 1.0 C8 A:8361201 3.2 85.0 1.0 C9 A:8361201 3.2 80.2 1.0 N01 A:8361201 3.2 81.4 1.0 CG A:GLN477 3.3 89.5 1.0 C2 A:8361201 3.4 93.6 1.0 CD A:GLN477 3.4 0.5 1.0 NE2 A:GLN477 3.4 0.7 1.0 O1 A:8361201 3.9 84.7 1.0 CG A:PRO513 4.0 79.0 1.0 OE1 A:GLN477 4.1 0.6 1.0 O A:TYR394 4.1 66.1 1.0 C10 A:8361201 4.1 80.1 1.0 CB A:TRP480 4.3 76.1 1.0 C14 A:8361201 4.3 79.2 1.0 C6 A:8361201 4.4 91.4 1.0 CE3 A:TRP480 4.4 76.8 1.0 CG A:GLU481 4.6 84.2 1.0 CB A:GLN477 4.7 79.7 1.0 C1 A:8361201 4.7 95.1 1.0 CD A:PRO513 4.8 75.5 1.0 N A:GLU481 5.0 75.8 1.0 O A:GLN477 5.0 83.2 1.0

Fluorine binding site 2 out of 6 in the 3.0A Syn Structure of the Multi-Domain Human Smoothened Receptor in Complex with TC114


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of 3.0A Syn Structure of the Multi-Domain Human Smoothened Receptor in Complex with TC114 within 5.0Å range: probe atom residue distance (Å) B Occ A:F1201 b:91.9 occ:1.00 F3 A:8361201 0.0 91.9 1.0 C4 A:8361201 1.4 91.4 1.0 F2 A:8361201 2.2 91.2 1.0 F4 A:8361201 2.2 91.9 1.0 C3 A:8361201 2.4 91.4 1.0 C2 A:8361201 2.7 93.6 1.0 N A:GLU481 3.1 75.8 1.0 C A:TRP480 3.2 80.4 1.0 CA A:GLU481 3.3 75.1 1.0 CG A:GLU481 3.4 84.2 1.0 O A:TRP480 3.4 79.7 1.0 CB A:TRP480 3.5 76.1 1.0 C5 A:8361201 3.8 89.2 1.0 CB A:GLU481 3.9 75.8 1.0 CA A:TRP480 4.0 78.2 1.0 CG A:GLN477 4.0 89.5 1.0 O A:GLN477 4.2 83.2 1.0 C1 A:8361201 4.2 95.1 1.0 CB A:PHE484 4.4 78.7 1.0 C8 A:8361201 4.4 85.0 1.0 NE2 A:GLN477 4.5 0.7 1.0 C A:GLU481 4.6 79.4 1.0 CD A:GLN477 4.7 0.5 1.0 CD A:GLU481 4.7 0.2 1.0 CG A:TRP480 4.9 77.3 1.0 CD1 A:LEU221 4.9 78.1 1.0 O1 A:8361201 4.9 84.7 1.0 O2 A:8361201 4.9 0.1 1.0 C6 A:8361201 4.9 91.4 1.0 N A:TRP480 4.9 79.3 1.0 CG A:PHE484 5.0 80.0 1.0

Fluorine binding site 3 out of 6 in the 3.0A Syn Structure of the Multi-Domain Human Smoothened Receptor in Complex with TC114


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of 3.0A Syn Structure of the Multi-Domain Human Smoothened Receptor in Complex with TC114 within 5.0Å range: probe atom residue distance (Å) B Occ A:F1201 b:91.9 occ:1.00 F4 A:8361201 0.0 91.9 1.0 C4 A:8361201 1.4 91.4 1.0 F3 A:8361201 2.2 91.9 1.0 F2 A:8361201 2.2 91.2 1.0 C3 A:8361201 2.4 91.4 1.0 C8 A:8361201 3.0 85.0 1.0 O1 A:8361201 3.0 84.7 1.0 C5 A:8361201 3.0 89.2 1.0 CD1 A:LEU221 3.3 78.1 1.0 CG A:PRO513 3.3 79.0 1.0 C2 A:8361201 3.4 93.6 1.0 CD A:PRO513 3.5 75.5 1.0 CB A:TRP480 3.8 76.1 1.0 N01 A:8361201 3.8 81.4 1.0 O A:TRP480 4.3 79.7 1.0 C6 A:8361201 4.3 91.4 1.0 C A:TRP480 4.4 80.4 1.0 C9 A:8361201 4.5 80.2 1.0 C10 A:8361201 4.5 80.1 1.0 CD2 A:PHE484 4.7 82.4 1.0 CG A:LEU221 4.7 78.7 1.0 C1 A:8361201 4.7 95.1 1.0 CA A:TRP480 4.7 78.2 1.0 CB A:PRO513 4.7 74.1 1.0 N A:PRO513 4.8 74.5 1.0 CG A:TRP480 4.8 77.3 1.0 N A:GLU481 4.8 75.8 1.0 CB A:PHE484 4.9 78.7 1.0 CE3 A:TRP480 5.0 76.8 1.0

Fluorine binding site 4 out of 6 in the 3.0A Syn Structure of the Multi-Domain Human Smoothened Receptor in Complex with TC114


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 4 of 3.0A Syn Structure of the Multi-Domain Human Smoothened Receptor in Complex with TC114 within 5.0Å range: probe atom residue distance (Å) B Occ B:F1201 b:79.2 occ:1.00 F2 B:8361201 0.0 79.2 1.0 C4 B:8361201 1.4 80.3 1.0 F4 B:8361201 2.2 81.2 1.0 F3 B:8361201 2.2 81.2 1.0 C3 B:8361201 2.4 80.5 1.0 C8 B:8361201 3.0 77.1 1.0 C5 B:8361201 3.0 79.1 1.0 N01 B:8361201 3.0 73.8 1.0 C9 B:8361201 3.2 71.9 1.0 C2 B:8361201 3.4 82.4 1.0 CG B:GLN477 3.5 73.1 1.0 CG B:PRO513 3.6 69.7 1.0 O1 B:8361201 3.6 77.8 1.0 CD B:GLN477 3.7 93.1 1.0 NE2 B:GLN477 3.8 81.0 1.0 C10 B:8361201 3.9 71.8 1.0 CB B:TRP480 4.1 67.2 1.0 C11 B:8361201 4.1 70.6 1.0 CE3 B:TRP480 4.2 67.6 1.0 C6 B:8361201 4.3 80.4 1.0 OE1 B:GLN477 4.3 92.9 1.0 CD B:PRO513 4.4 66.2 1.0 O B:TYR394 4.5 71.4 1.0 CB B:PRO513 4.7 65.3 1.0 C1 B:8361201 4.7 84.8 1.0 CB B:GLN477 4.8 67.6 1.0 CD2 B:TRP480 4.9 67.4 1.0 CG B:GLU481 4.9 79.0 1.0 CG B:TRP480 5.0 68.2 1.0

Fluorine binding site 5 out of 6 in the 3.0A Syn Structure of the Multi-Domain Human Smoothened Receptor in Complex with TC114


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 5 of 3.0A Syn Structure of the Multi-Domain Human Smoothened Receptor in Complex with TC114 within 5.0Å range: probe atom residue distance (Å) B Occ B:F1201 b:81.2 occ:1.00 F3 B:8361201 0.0 81.2 1.0 C4 B:8361201 1.4 80.3 1.0 F2 B:8361201 2.2 79.2 1.0 F4 B:8361201 2.2 81.2 1.0 C3 B:8361201 2.4 80.5 1.0 C2 B:8361201 2.6 82.4 1.0 N B:GLU481 3.0 69.6 1.0 C B:TRP480 3.1 73.1 1.0 CB B:TRP480 3.3 67.2 1.0 CA B:GLU481 3.3 69.3 1.0 CG B:GLU481 3.4 79.0 1.0 O B:TRP480 3.4 72.5 1.0 CG B:GLN477 3.8 73.1 1.0 CA B:TRP480 3.8 69.4 1.0 C5 B:8361201 3.8 79.1 1.0 CB B:GLU481 3.9 69.9 1.0 O B:GLN477 3.9 74.8 1.0 C1 B:8361201 4.2 84.8 1.0 NE2 B:GLN477 4.4 81.0 1.0 C8 B:8361201 4.4 77.1 1.0 CD B:GLN477 4.5 93.1 1.0 CG B:TRP480 4.6 68.2 1.0 CB B:PHE484 4.6 72.8 1.0 C B:GLU481 4.7 74.3 1.0 N B:TRP480 4.7 69.8 1.0 CD B:GLU481 4.7 0.3 1.0 O2 B:8361201 4.7 93.3 1.0 C6 B:8361201 4.8 80.4 1.0 CG B:PRO513 4.9 69.7 1.0 O1 B:8361201 4.9 77.8 1.0 CE3 B:TRP480 4.9 67.6 1.0 C B:GLN477 4.9 73.8 1.0 OE2 B:GLU481 5.0 96.1 1.0 CD1 B:LEU221 5.0 74.9 1.0 N1 B:8361201 5.0 91.2 1.0 N01 B:8361201 5.0 73.8 1.0 C7 B:8361201 5.0 82.2 1.0

Fluorine binding site 6 out of 6 in the 3.0A Syn Structure of the Multi-Domain Human Smoothened Receptor in Complex with TC114


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 6 of 3.0A Syn Structure of the Multi-Domain Human Smoothened Receptor in Complex with TC114 within 5.0Å range: probe atom residue distance (Å) B Occ B:F1201 b:81.2 occ:1.00 F4 B:8361201 0.0 81.2 1.0 C4 B:8361201 1.4 80.3 1.0 F2 B:8361201 2.2 79.2 1.0 F3 B:8361201 2.2 81.2 1.0 C3 B:8361201 2.4 80.5 1.0 CD1 B:LEU221 3.1 74.9 1.0 C5 B:8361201 3.1 79.1 1.0 O1 B:8361201 3.2 77.8 1.0 C8 B:8361201 3.2 77.1 1.0 CG B:PRO513 3.3 69.7 1.0 C2 B:8361201 3.3 82.4 1.0 CD B:PRO513 3.3 66.2 1.0 CB B:TRP480 3.5 67.2 1.0 O B:TRP480 4.0 72.5 1.0 N01 B:8361201 4.1 73.8 1.0 C B:TRP480 4.1 73.1 1.0 C6 B:8361201 4.4 80.4 1.0 CA B:TRP480 4.4 69.4 1.0 CG B:LEU221 4.5 75.4 1.0 CG B:TRP480 4.6 68.2 1.0 N B:PRO513 4.6 65.2 1.0 N B:GLU481 4.6 69.6 1.0 C1 B:8361201 4.6 84.8 1.0 CD2 B:PHE484 4.7 76.8 1.0 CB B:PRO513 4.7 65.3 1.0 C9 B:8361201 4.8 71.9 1.0 C10 B:8361201 4.8 71.8 1.0 CB B:PHE484 4.8 72.8 1.0 CE3 B:TRP480 4.9 67.6 1.0

X.Zhang, F.Zhao, Y.Wu, J.Yang, G.W.Han, S.Zhao, A.Ishchenko, L.Ye, X.Lin, K.Ding, V.Dharmarajan, P.R.Griffin, C.Gati, G.Nelson, M.S.Hunter, M.A.Hanson, V.Cherezov, R.C.Stevens, W.Tan, H.Tao, F.Xu. Crystal Structure of A Multi-Domain Human Smoothened Receptor in Complex with A Super Stabilizing Ligand. Nat Commun V. 8 15383 2017.
ISSN: ESSN 2041-1723
PubMed: 28513578
DOI: 10.1038/NCOMMS15383