Fluorine in PDB 7svo: DPP8 in Complex with Ligand Iced-1

All present enzymatic activity of DPP8 in Complex with Ligand Iced-1:
3.4.14.5;

The structure of DPP8 in Complex with Ligand Iced-1, PDB code: 7svo was solved by A.Lammens, K.Hollenstein, D.J.Klein, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	135.77 / 2.58
Space group	C 2 2 21
Cell size a, b, c (Å), α, β, γ (°)	162.816, 246.016, 261.767, 90, 90, 90
R / Rfree (%)	18 / 20.8

The binding sites of Fluorine atom in the DPP8 in Complex with Ligand Iced-1 (pdb code 7svo). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 3 binding sites of Fluorine where determined in the DPP8 in Complex with Ligand Iced-1, PDB code: 7svo:
Jump to Fluorine binding site number: 1; 2; 3;

Fluorine binding site 1 out of 3 in the DPP8 in Complex with Ligand Iced-1


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of DPP8 in Complex with Ligand Iced-1 within 5.0Å range: probe atom residue distance (Å) B Occ A:F901 b:45.3 occ:1.00 F19 A:CW8901 0.0 45.3 1.0 C17 A:CW8901 1.4 43.7 1.0 C20 A:CW8901 2.3 46.6 1.0 C16 A:CW8901 2.4 39.4 1.0 C21 A:CW8901 3.0 39.0 1.0 C23 A:CW8901 3.1 32.1 1.0 N15 A:CW8901 3.2 42.7 1.0 N24 A:CW8901 3.2 35.5 1.0 CD2 A:TYR756 3.4 42.3 1.0 CB A:TYR756 3.5 46.7 1.0 N A:TYR756 3.5 42.4 1.0 CA A:TYR756 3.6 42.3 1.0 OG A:SER755 3.8 43.3 1.0 OH A:TYR791 3.8 42.4 1.0 CG A:TYR756 3.9 45.7 1.0 CH2 A:TRP784 4.1 47.1 1.0 CG2 A:VAL781 4.2 49.9 1.0 C A:SER755 4.2 42.5 1.0 CZ A:TYR791 4.3 46.1 1.0 C13 A:CW8901 4.4 36.3 1.0 CE2 A:TYR756 4.5 45.6 1.0 CE1 A:TYR791 4.5 44.7 1.0 O A:HOH1095 4.6 40.9 1.0 OH A:TYR669 4.7 45.3 1.0 CB A:SER755 4.7 42.3 1.0 CZ3 A:TRP784 4.8 47.1 1.0 O A:SER755 4.8 36.9 1.0 CA A:SER755 4.9 41.1 1.0 CZ2 A:TRP784 5.0 42.0 1.0

Fluorine binding site 2 out of 3 in the DPP8 in Complex with Ligand Iced-1


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of DPP8 in Complex with Ligand Iced-1 within 5.0Å range: probe atom residue distance (Å) B Occ B:F901 b:43.4 occ:1.00 F19 B:CW8901 0.0 43.4 1.0 C17 B:CW8901 1.4 45.2 1.0 C20 B:CW8901 2.3 42.9 1.0 C16 B:CW8901 2.4 38.7 1.0 C21 B:CW8901 3.0 38.6 1.0 C23 B:CW8901 3.1 40.1 1.0 N15 B:CW8901 3.2 40.6 1.0 N24 B:CW8901 3.3 44.4 1.0 CD2 B:TYR756 3.3 45.0 1.0 CB B:TYR756 3.6 42.5 1.0 N B:TYR756 3.6 38.6 1.0 CA B:TYR756 3.7 40.8 1.0 OH B:TYR791 3.7 37.1 1.0 CG B:TYR756 3.9 44.5 1.0 OG B:SER755 3.9 39.9 1.0 CG2 B:VAL781 4.0 52.0 1.0 CH2 B:TRP784 4.1 45.0 1.0 CZ B:TYR791 4.2 41.0 1.0 C B:SER755 4.3 42.8 1.0 CE2 B:TYR756 4.4 50.3 1.0 CE1 B:TYR791 4.4 39.0 1.0 C13 B:CW8901 4.4 42.0 1.0 OH B:TYR669 4.6 46.4 1.0 O B:HOH1048 4.6 34.8 1.0 CZ3 B:TRP784 4.8 43.1 1.0 CB B:SER755 4.8 47.9 1.0 CE2 B:TYR791 4.9 45.3 1.0 O B:SER755 5.0 46.8 1.0

Fluorine binding site 3 out of 3 in the DPP8 in Complex with Ligand Iced-1


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of DPP8 in Complex with Ligand Iced-1 within 5.0Å range: probe atom residue distance (Å) B Occ C:F901 b:46.8 occ:1.00 F19 C:CW8901 0.0 46.8 1.0 C17 C:CW8901 1.4 44.1 1.0 C20 C:CW8901 2.3 45.7 1.0 C16 C:CW8901 2.4 45.7 1.0 C21 C:CW8901 3.0 36.2 1.0 C23 C:CW8901 3.1 33.2 1.0 N24 C:CW8901 3.1 28.6 1.0 N15 C:CW8901 3.1 39.5 1.0 CD2 C:TYR756 3.2 38.2 1.0 CB C:TYR756 3.3 39.6 1.0 N C:TYR756 3.5 43.7 1.0 CA C:TYR756 3.6 45.0 1.0 OH C:TYR791 3.7 35.8 1.0 CG C:TYR756 3.7 37.2 1.0 OG C:SER755 3.9 37.4 1.0 CZ C:TYR791 4.1 36.7 1.0 CH2 C:TRP784 4.2 40.2 1.0 CG2 C:VAL781 4.2 48.3 1.0 C C:SER755 4.3 44.0 1.0 C13 C:CW8901 4.4 43.6 1.0 CE2 C:TYR756 4.4 41.2 1.0 CE1 C:TYR791 4.4 38.5 1.0 O C:HOH1056 4.5 32.9 1.0 OH C:TYR669 4.5 40.5 1.0 CB C:SER755 4.8 42.8 1.0 CZ3 C:TRP784 4.9 39.7 1.0 CE2 C:TYR791 4.9 37.0 1.0 O C:SER755 4.9 44.0 1.0

K.P.Moore, A.G.Schwaid, M.Tudor, S.Park, D.C.Beshore, A.Converso, W.D.Shipe, R.Anand, P.Lan, R.Moningka, D.M.Rothman, W.Sun, A.Chi, I.Cornella-Taracido, G.C.Adam, C.Bahnck-Teets, S.S.Carroll, J.F.Fay, S.L.Goh, J.Lusen, S.Quan, S.Rodriguez, M.Xu, C.L.Andrews, C.Song, T.Filzen, J.Li, K.Hollenstein, D.J.Klein, A.Lammens, U.M.Lim, Z.Fang, C.Mchale, Y.Li, M.Lu, T.L.Diamond, B.J.Howell, P.Zuck, C.J.Balibar. A Phenotypic Screen Identifies Potent DPP9 Inhibitors Capable of Killing Hiv-1 Infected Cells. Acs Chem.Biol. V. 17 2595 2022.
ISSN: ESSN 1554-8937
PubMed: 36044633
DOI: 10.1021/ACSCHEMBIO.2C00515