Fluorine in PDB 5fbe: Complement Factor D in Complex with COMPOUND2

All present enzymatic activity of Complement Factor D in Complex with COMPOUND2:
3.4.21.46;

The structure of Complement Factor D in Complex with COMPOUND2, PDB code: 5fbe was solved by N.Ostermann, F.Zink, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	16.10 / 1.43
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	55.400, 50.000, 39.358, 90.00, 105.75, 90.00
R / Rfree (%)	16.9 / 18.8

The binding sites of Fluorine atom in the Complement Factor D in Complex with COMPOUND2 (pdb code 5fbe). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 3 binding sites of Fluorine where determined in the Complement Factor D in Complex with COMPOUND2, PDB code: 5fbe:
Jump to Fluorine binding site number: 1; 2; 3;

Fluorine binding site 1 out of 3 in the Complement Factor D in Complex with COMPOUND2


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of Complement Factor D in Complex with COMPOUND2 within 5.0Å range: probe atom residue distance (Å) B Occ A:F302 b:36.8 occ:1.00 F19 A:5W5302 0.0 36.8 1.0 C5 A:5W5302 1.4 40.0 1.0 F20 A:5W5302 2.2 43.6 1.0 O10 A:5W5302 2.3 35.5 1.0 F21 A:5W5302 2.3 38.0 1.0 C18 A:5W5302 2.9 35.0 1.0 CG A:ARG151 3.1 23.0 1.0 C29 A:5W5302 3.1 37.9 1.0 CD A:ARG151 3.2 40.0 1.0 O A:HOH464 3.3 18.6 1.0 CG2 A:ILE143 3.5 15.0 1.0 C15 A:5W5302 4.0 31.9 1.0 O A:HOH452 4.1 36.0 1.0 CB A:ARG151 4.2 18.6 1.0 C26 A:5W5302 4.4 37.1 1.0 NE A:ARG151 4.5 51.5 1.0 N A:ILE143 4.6 12.8 1.0 O A:LYS192 4.7 17.4 1.0 O A:GLY149 4.8 17.0 1.0 CB A:ILE143 4.8 14.2 1.0 C13 A:5W5302 4.9 34.4 1.0 CA A:ARG151 5.0 16.2 1.0

Fluorine binding site 2 out of 3 in the Complement Factor D in Complex with COMPOUND2


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of Complement Factor D in Complex with COMPOUND2 within 5.0Å range: probe atom residue distance (Å) B Occ A:F302 b:43.6 occ:1.00 F20 A:5W5302 0.0 43.6 1.0 C5 A:5W5302 1.4 40.0 1.0 F19 A:5W5302 2.2 36.8 1.0 F21 A:5W5302 2.2 38.0 1.0 O10 A:5W5302 2.2 35.5 1.0 C18 A:5W5302 2.9 35.0 1.0 O A:LYS192 3.1 17.4 1.0 C15 A:5W5302 3.2 31.9 1.0 CA A:GLY193 3.2 14.0 1.0 CA A:GLY142 3.5 13.6 1.0 N A:ILE143 3.7 12.8 1.0 C A:LYS192 3.7 17.3 1.0 N A:GLY193 3.8 14.9 1.0 CG2 A:ILE143 3.9 15.0 1.0 C A:GLY142 3.9 13.9 1.0 C29 A:5W5302 3.9 37.9 1.0 O A:TRP141 4.0 13.3 1.0 C A:GLY193 4.3 14.0 1.0 C13 A:5W5302 4.4 34.4 1.0 CD2 A:HIS40 4.5 13.2 1.0 N A:GLY142 4.5 13.2 1.0 C A:TRP141 4.6 14.0 1.0 CA A:ILE143 4.6 12.9 1.0 CG A:LYS192 4.7 25.6 1.0 O A:GLY193 4.7 14.1 1.0 O A:HOH452 4.7 36.0 1.0 CG A:ARG151 4.8 23.0 1.0 CB A:ILE143 4.8 14.2 1.0 O A:GLY142 4.9 14.6 1.0 NE2 A:HIS40 4.9 12.7 1.0 CD A:ARG151 4.9 40.0 1.0 C26 A:5W5302 5.0 37.1 1.0 CA A:LYS192 5.0 15.4 1.0 CB A:LYS192 5.0 16.6 1.0

Fluorine binding site 3 out of 3 in the Complement Factor D in Complex with COMPOUND2


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of Complement Factor D in Complex with COMPOUND2 within 5.0Å range: probe atom residue distance (Å) B Occ A:F302 b:38.0 occ:1.00 F21 A:5W5302 0.0 38.0 1.0 C5 A:5W5302 1.4 40.0 1.0 F20 A:5W5302 2.2 43.6 1.0 O10 A:5W5302 2.3 35.5 1.0 F19 A:5W5302 2.3 36.8 1.0 O A:TRP141 3.1 13.3 1.0 O A:HOH475 3.2 15.2 1.0 CG A:ARG151 3.3 23.0 1.0 CD A:ARG151 3.3 40.0 1.0 O A:HOH452 3.4 36.0 1.0 C18 A:5W5302 3.6 35.0 1.0 CB A:ARG151 3.6 18.6 1.0 O A:HOH467 3.7 21.5 1.0 CD2 A:HIS40 4.0 13.2 1.0 C A:TRP141 4.2 14.0 1.0 CA A:GLY142 4.3 13.6 1.0 CA A:ARG151 4.3 16.2 1.0 C A:GLY142 4.4 13.9 1.0 C15 A:5W5302 4.4 31.9 1.0 C29 A:5W5302 4.5 37.9 1.0 N A:ILE143 4.5 12.8 1.0 CG2 A:ILE143 4.7 15.0 1.0 N A:GLY142 4.7 13.2 1.0 NE A:ARG151 4.8 51.5 1.0 CD A:PRO152 4.8 13.5 1.0 O A:GLY142 4.9 14.6 1.0 CG A:HIS40 4.9 12.7 1.0 NE2 A:HIS40 4.9 12.7 1.0

J.Maibaum, S.M.Liao, A.Vulpetti, N.Ostermann, S.Randl, S.Rudisser, E.Lorthiois, P.Erbel, B.Kinzel, F.A.Kolb, S.Barbieri, J.Wagner, C.Durand, K.Fettis, S.Dussauge, N.Hughes, O.Delgado, U.Hommel, T.Gould, A.Mac Sweeney, B.Gerhartz, F.Cumin, S.Flohr, A.Schubart, B.Jaffee, R.Harrison, A.M.Risitano, J.Eder, K.Anderson. Small-Molecule Factor D Inhibitors Targeting the Alternative Complement Pathway. Nat.Chem.Biol. V. 12 1105 2016.
ISSN: ESSN 1552-4469
PubMed: 27775713
DOI: 10.1038/NCHEMBIO.2208