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Fluorine in PDB 5nba: Complement Factor D in Complex with the Inhibitor (2S,4R)-4-Fluoro- Pyrrolidine-1,2-Dicarboxylic Acid 1-[(1-Carbamoyl-1H-Indol-3-Yl)- Amide] 2-[(3-Trifluoromethoxy-Phenyl)-Amide]

Enzymatic activity of Complement Factor D in Complex with the Inhibitor (2S,4R)-4-Fluoro- Pyrrolidine-1,2-Dicarboxylic Acid 1-[(1-Carbamoyl-1H-Indol-3-Yl)- Amide] 2-[(3-Trifluoromethoxy-Phenyl)-Amide]

All present enzymatic activity of Complement Factor D in Complex with the Inhibitor (2S,4R)-4-Fluoro- Pyrrolidine-1,2-Dicarboxylic Acid 1-[(1-Carbamoyl-1H-Indol-3-Yl)- Amide] 2-[(3-Trifluoromethoxy-Phenyl)-Amide]:
3.4.21.46;

Protein crystallography data

The structure of Complement Factor D in Complex with the Inhibitor (2S,4R)-4-Fluoro- Pyrrolidine-1,2-Dicarboxylic Acid 1-[(1-Carbamoyl-1H-Indol-3-Yl)- Amide] 2-[(3-Trifluoromethoxy-Phenyl)-Amide], PDB code: 5nba was solved by A.Mac Sweeney, N.Ostermann, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 53.07 / 1.87
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 55.437, 49.727, 39.026, 90.00, 106.82, 90.00
R / Rfree (%) 17.3 / 26

Fluorine Binding Sites:

The binding sites of Fluorine atom in the Complement Factor D in Complex with the Inhibitor (2S,4R)-4-Fluoro- Pyrrolidine-1,2-Dicarboxylic Acid 1-[(1-Carbamoyl-1H-Indol-3-Yl)- Amide] 2-[(3-Trifluoromethoxy-Phenyl)-Amide] (pdb code 5nba). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 4 binding sites of Fluorine where determined in the Complement Factor D in Complex with the Inhibitor (2S,4R)-4-Fluoro- Pyrrolidine-1,2-Dicarboxylic Acid 1-[(1-Carbamoyl-1H-Indol-3-Yl)- Amide] 2-[(3-Trifluoromethoxy-Phenyl)-Amide], PDB code: 5nba:
Jump to Fluorine binding site number: 1; 2; 3; 4;

Fluorine binding site 1 out of 4 in 5nba

Go back to Fluorine Binding Sites List in 5nba
Fluorine binding site 1 out of 4 in the Complement Factor D in Complex with the Inhibitor (2S,4R)-4-Fluoro- Pyrrolidine-1,2-Dicarboxylic Acid 1-[(1-Carbamoyl-1H-Indol-3-Yl)- Amide] 2-[(3-Trifluoromethoxy-Phenyl)-Amide]


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 the Inhibitor (2S,4R)-4-Fluoro- Pyrrolidine-1,2-Dicarboxylic Acid 1-[(1-Carbamoyl-1H-Indol-3-Yl)- Amide] 2-[(3-Trifluoromethoxy-Phenyl)-Amide] within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F301

b:15.3
occ:1.00
 F1 A:8S5301 0.0 15.3 1.0
C4 A:8S5301 1.4 14.0 1.0
C5 A:8S5301 2.4 13.6 1.0
C3 A:8S5301 2.4 13.3 1.0
N1 A:8S5301 2.9 13.5 1.0
C2 A:8S5301 3.0 12.9 1.0
N A:CYS58 3.0 17.3 1.0
C A:HIS57 3.1 19.7 1.0
CA A:CYS58 3.2 17.9 1.0
O A:HIS57 3.3 16.9 1.0
CB A:SER215 3.4 17.5 1.0
SG A:CYS42 3.5 12.1 1.0
SG A:CYS58 3.5 12.2 1.0
CB A:HIS57 3.9 25.3 1.0
CB A:CYS58 3.9 14.4 1.0
C6 A:8S5301 4.0 13.9 1.0
CA A:HIS57 4.0 21.0 1.0
OG A:SER215 4.1 20.2 1.0
O A:SER215 4.3 18.9 1.0
CB A:SER195 4.4 13.8 1.0
C A:CYS58 4.4 21.2 1.0
CA A:SER215 4.5 15.9 1.0
C1 A:8S5301 4.5 14.2 1.0
N2 A:8S5301 4.6 15.1 1.0
N A:HIS57 4.6 17.8 1.0
O3 A:8S5301 4.8 12.8 1.0
OG A:SER195 4.8 17.2 1.0
O A:CYS58 4.8 25.0 1.0
C A:SER215 4.9 17.3 1.0

Fluorine binding site 2 out of 4 in 5nba

Go back to Fluorine Binding Sites List in 5nba
Fluorine binding site 2 out of 4 in the Complement Factor D in Complex with the Inhibitor (2S,4R)-4-Fluoro- Pyrrolidine-1,2-Dicarboxylic Acid 1-[(1-Carbamoyl-1H-Indol-3-Yl)- Amide] 2-[(3-Trifluoromethoxy-Phenyl)-Amide]


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 the Inhibitor (2S,4R)-4-Fluoro- Pyrrolidine-1,2-Dicarboxylic Acid 1-[(1-Carbamoyl-1H-Indol-3-Yl)- Amide] 2-[(3-Trifluoromethoxy-Phenyl)-Amide] within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F301

b:18.5
occ:1.00
 F2 A:8S5301 0.0 18.5 1.0
C21 A:8S5301 1.3 18.4 1.0
O4 A:8S5301 2.1 17.3 1.0
F4 A:8S5301 2.1 19.9 1.0
F3 A:8S5301 2.2 20.5 1.0
O A:HOH467 3.0 10.0 1.0
O A:TRP141 3.2 10.5 1.0
C20 A:8S5301 3.5 18.2 1.0
CG A:ARG151 3.5 17.5 1.0
O A:HOH519 3.6 11.4 1.0
CB A:ARG151 3.7 16.5 1.0
CD A:ARG151 4.0 20.3 1.0
CD2 A:HIS40 4.1 10.7 1.0
C19 A:8S5301 4.3 18.3 1.0
C22 A:8S5301 4.3 16.1 1.0
CA A:ARG151 4.3 14.9 1.0
C A:TRP141 4.4 10.7 1.0
O A:HOH435 4.4 17.8 1.0
C A:GLY142 4.5 11.9 1.0
CA A:GLY142 4.5 11.7 1.0
N A:ILE143 4.6 12.2 1.0
CG2 A:ILE143 4.8 13.8 1.0
CD A:PRO152 4.8 12.2 1.0
O A:GLY142 4.9 10.9 1.0
CG A:HIS40 4.9 10.5 1.0
O A:HIS40 4.9 11.8 1.0
N A:GLY142 4.9 11.8 1.0

Fluorine binding site 3 out of 4 in 5nba

Go back to Fluorine Binding Sites List in 5nba
Fluorine binding site 3 out of 4 in the Complement Factor D in Complex with the Inhibitor (2S,4R)-4-Fluoro- Pyrrolidine-1,2-Dicarboxylic Acid 1-[(1-Carbamoyl-1H-Indol-3-Yl)- Amide] 2-[(3-Trifluoromethoxy-Phenyl)-Amide]


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 the Inhibitor (2S,4R)-4-Fluoro- Pyrrolidine-1,2-Dicarboxylic Acid 1-[(1-Carbamoyl-1H-Indol-3-Yl)- Amide] 2-[(3-Trifluoromethoxy-Phenyl)-Amide] within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F301

b:20.5
occ:1.00
 F3 A:8S5301 0.0 20.5 1.0
C21 A:8S5301 1.3 18.4 1.0
F4 A:8S5301 2.1 19.9 1.0
F2 A:8S5301 2.2 18.5 1.0
O4 A:8S5301 2.2 17.3 1.0
C20 A:8S5301 2.8 18.2 1.0
C22 A:8S5301 3.1 16.1 1.0
CA A:GLY193 3.4 13.2 1.0
O A:LYS192 3.4 15.1 1.0
CA A:GLY142 3.6 11.7 1.0
N A:ILE143 3.7 12.2 1.0
O A:TRP141 3.8 10.5 1.0
C19 A:8S5301 3.9 18.3 1.0
C A:GLY142 3.9 11.9 1.0
C A:LYS192 3.9 14.2 1.0
N A:GLY193 4.0 13.9 1.0
CG2 A:ILE143 4.0 13.8 1.0
CD2 A:HIS40 4.3 10.7 1.0
C16 A:8S5301 4.3 15.7 1.0
C A:GLY193 4.4 13.2 1.0
N A:GLY142 4.5 11.8 1.0
C A:TRP141 4.5 10.7 1.0
CA A:ILE143 4.7 13.3 1.0
O A:GLY193 4.7 11.6 1.0
NE2 A:HIS40 4.8 9.5 1.0
O A:GLY142 4.8 10.9 1.0
CG A:LYS192 4.8 20.9 1.0
O A:HOH467 4.9 10.0 1.0
C18 A:8S5301 4.9 18.5 1.0
CG A:ARG151 4.9 17.5 1.0
CB A:ILE143 4.9 12.9 1.0

Fluorine binding site 4 out of 4 in 5nba

Go back to Fluorine Binding Sites List in 5nba
Fluorine binding site 4 out of 4 in the Complement Factor D in Complex with the Inhibitor (2S,4R)-4-Fluoro- Pyrrolidine-1,2-Dicarboxylic Acid 1-[(1-Carbamoyl-1H-Indol-3-Yl)- Amide] 2-[(3-Trifluoromethoxy-Phenyl)-Amide]


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 4 of Complement Factor D in Complex with the Inhibitor (2S,4R)-4-Fluoro- Pyrrolidine-1,2-Dicarboxylic Acid 1-[(1-Carbamoyl-1H-Indol-3-Yl)- Amide] 2-[(3-Trifluoromethoxy-Phenyl)-Amide] within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F301

b:19.9
occ:1.00
 F4 A:8S5301 0.0 19.9 1.0
C21 A:8S5301 1.3 18.4 1.0
F3 A:8S5301 2.1 20.5 1.0
F2 A:8S5301 2.1 18.5 1.0
O4 A:8S5301 2.2 17.3 1.0
C20 A:8S5301 2.7 18.2 1.0
C19 A:8S5301 3.1 18.3 1.0
CG A:ARG151 3.3 17.5 1.0
CG2 A:ILE143 3.5 13.8 1.0
CD A:ARG151 3.7 20.3 1.0
C22 A:8S5301 3.7 16.1 1.0
C18 A:8S5301 4.2 18.5 1.0
CB A:ARG151 4.3 16.5 1.0
N A:ILE143 4.5 12.2 1.0
C16 A:8S5301 4.7 15.7 1.0
CB A:ILE143 4.8 12.9 1.0
O A:LYS192 4.9 15.1 1.0
CA A:ARG151 4.9 14.9 1.0
CA A:ILE143 4.9 13.3 1.0
O A:HOH435 4.9 17.8 1.0
C17 A:8S5301 5.0 17.6 1.0
O A:TRP141 5.0 10.5 1.0

Reference:

E.Lorthiois, K.Anderson, A.Vulpetti, O.Rogel, F.Cumin, N.Ostermann, S.Steinbacher, A.Mac Sweeney, O.Delgado, S.M.Liao, S.Randl, S.Rudisser, S.Dussauge, K.Fettis, L.Kieffer, A.De Erkenez, L.Yang, C.Hartwieg, U.A.Argikar, L.R.La Bonte, R.Newton, V.Kansara, S.Flohr, U.Hommel, B.Jaffee, J.Maibaum. Discovery of Highly Potent and Selective Small-Molecule Reversible Factor D Inhibitors Demonstrating Alternative Complement Pathway Inhibition in Vivo. J. Med. Chem. V. 60 5717 2017.
ISSN: ISSN 1520-4804
PubMed: 28621538
DOI: 10.1021/ACS.JMEDCHEM.7B00425
Page generated: Tue Jul 15 05:28:12 2025

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