Fluorine in PDB 7svn: DPP9 in Complex with Ligand Iced-1

All present enzymatic activity of DPP9 in Complex with Ligand Iced-1:
3.4.14.5;

The structure of DPP9 in Complex with Ligand Iced-1, PDB code: 7svn 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)	157.52 / 2.78
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	119.789, 117.439, 163.455, 90, 105.49, 90
R / Rfree (%)	26.7 / 34.9

The binding sites of Fluorine atom in the DPP9 in Complex with Ligand Iced-1 (pdb code 7svn). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 4 binding sites of Fluorine where determined in the DPP9 in Complex with Ligand Iced-1, PDB code: 7svn:
Jump to Fluorine binding site number: 1; 2; 3; 4;

Fluorine binding site 1 out of 4 in the DPP9 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 DPP9 in Complex with Ligand Iced-1 within 5.0Å range: probe atom residue distance (Å) B Occ A:F901 b:40.0 occ:1.00 F19 A:CW8901 0.0 40.0 1.0 C17 A:CW8901 1.4 31.7 1.0 C20 A:CW8901 2.3 31.2 1.0 C16 A:CW8901 2.4 28.6 1.0 C21 A:CW8901 3.0 35.3 1.0 C23 A:CW8901 3.1 39.3 1.0 N15 A:CW8901 3.1 32.8 1.0 CD2 A:TYR731 3.4 19.9 1.0 CB A:TYR731 3.5 19.4 1.0 OG A:SER730 3.6 50.4 1.0 N A:TYR731 3.6 19.6 1.0 N24 A:CW8901 3.6 32.4 1.0 CA A:TYR731 3.7 18.7 1.0 OH A:TYR766 3.8 23.9 1.0 CG A:TYR731 3.9 17.5 1.0 CG2 A:VAL756 4.0 22.2 1.0 OH A:TYR644 4.1 46.2 1.0 CZ A:TYR766 4.2 26.9 1.0 CH2 A:TRP759 4.3 18.4 1.0 O A:HOH1033 4.3 12.0 1.0 C A:SER730 4.3 27.4 1.0 C13 A:CW8901 4.4 45.0 1.0 CE2 A:TYR731 4.5 23.3 1.0 CB A:SER730 4.6 37.1 1.0 CE1 A:TYR766 4.6 22.5 1.0 CE2 A:TYR766 4.7 33.8 1.0 O A:SER730 4.9 28.6 1.0 CZ A:TYR644 4.9 42.1 1.0 CZ3 A:TRP759 4.9 16.7 1.0 CA A:SER730 5.0 32.0 1.0

Fluorine binding site 2 out of 4 in the DPP9 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 DPP9 in Complex with Ligand Iced-1 within 5.0Å range: probe atom residue distance (Å) B Occ B:F901 b:51.8 occ:1.00 F19 B:CW8901 0.0 51.8 1.0 C17 B:CW8901 1.4 53.8 1.0 C16 B:CW8901 2.4 56.4 1.0 C20 B:CW8901 2.4 51.2 1.0 C23 B:CW8901 2.9 35.1 1.0 C21 B:CW8901 2.9 44.8 1.0 N15 B:CW8901 3.1 54.8 1.0 CB B:TYR731 3.3 25.4 1.0 N B:TYR731 3.3 23.9 1.0 N24 B:CW8901 3.3 23.7 1.0 OG B:SER730 3.4 36.3 1.0 O B:HOH1002 3.4 7.4 1.0 CD2 B:TYR731 3.5 25.9 1.0 OH B:TYR644 3.5 40.7 1.0 CA B:TYR731 3.6 24.6 1.0 OH B:TYR766 3.7 17.3 1.0 CG B:TYR731 3.9 22.5 1.0 C B:SER730 4.1 23.8 1.0 CG2 B:VAL756 4.2 42.6 1.0 CZ B:TYR766 4.3 20.8 1.0 CB B:SER730 4.3 32.2 1.0 C13 B:CW8901 4.3 64.8 1.0 CZ B:TYR644 4.3 58.0 1.0 CE1 B:TYR644 4.6 53.0 1.0 CE2 B:TYR731 4.7 25.5 1.0 CE2 B:TYR766 4.7 24.7 1.0 CA B:SER730 4.8 28.0 1.0 O B:SER730 4.8 24.4 1.0 CH2 B:TRP759 4.9 14.1 1.0 CE1 B:TYR766 4.9 16.4 1.0

Fluorine binding site 3 out of 4 in the DPP9 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 DPP9 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 33.4 1.0 C20 C:CW8901 2.3 37.1 1.0 C16 C:CW8901 2.4 34.0 1.0 C23 C:CW8901 2.9 38.1 1.0 N24 C:CW8901 2.9 21.5 1.0 C21 C:CW8901 2.9 36.9 1.0 N15 C:CW8901 3.1 43.6 1.0 CB C:TYR731 3.3 21.6 1.0 CD2 C:TYR731 3.3 19.3 1.0 N C:TYR731 3.3 32.9 1.0 CA C:TYR731 3.5 24.3 1.0 OG C:SER730 3.6 30.2 1.0 OH C:TYR766 3.7 15.2 1.0 CG C:TYR731 3.8 19.6 1.0 OH C:TYR644 4.0 26.0 1.0 CG2 C:VAL756 4.0 69.2 1.0 C C:SER730 4.1 36.1 1.0 CZ C:TYR766 4.2 13.7 1.0 CH2 C:TRP759 4.3 17.3 1.0 C13 C:CW8901 4.4 50.3 1.0 CE2 C:TYR731 4.5 21.3 1.0 CB C:SER730 4.5 29.4 1.0 O C:SER730 4.6 30.0 1.0 CZ C:TYR644 4.7 21.6 1.0 CE1 C:TYR766 4.7 12.6 1.0 CA C:SER730 4.8 30.6 1.0 CE2 C:TYR766 4.9 14.9 1.0 CE1 C:TYR644 4.9 21.9 1.0

Fluorine binding site 4 out of 4 in the DPP9 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 4 of DPP9 in Complex with Ligand Iced-1 within 5.0Å range: probe atom residue distance (Å) B Occ D:F901 b:38.2 occ:1.00 F19 D:CW8901 0.0 38.2 1.0 C17 D:CW8901 1.4 31.0 1.0 C16 D:CW8901 2.3 30.9 1.0 C20 D:CW8901 2.3 32.4 1.0 N24 D:CW8901 2.9 22.9 1.0 C21 D:CW8901 3.0 37.5 1.0 C23 D:CW8901 3.1 46.0 1.0 N15 D:CW8901 3.1 34.1 1.0 CD2 D:TYR731 3.2 24.3 1.0 OH D:TYR766 3.3 11.5 1.0 CB D:TYR731 3.5 31.4 1.0 CZ D:TYR766 3.8 14.4 1.0 CG D:TYR731 3.8 23.8 1.0 CA D:TYR731 3.9 28.7 1.0 CH2 D:TRP759 3.9 16.6 1.0 N D:TYR731 3.9 32.3 1.0 CG2 D:VAL756 4.0 29.9 1.0 OG D:SER730 4.1 46.2 1.0 CE1 D:TYR766 4.2 14.7 1.0 O D:HOH1032 4.2 8.9 1.0 CE2 D:TYR731 4.3 27.2 1.0 OH D:TYR644 4.3 21.6 1.0 C13 D:CW8901 4.4 46.4 1.0 CE2 D:TYR766 4.4 15.3 1.0 CZ3 D:TRP759 4.6 13.8 1.0 C D:SER730 4.7 36.9 1.0 CZ2 D:TRP759 4.9 17.6 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