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

Enzymatic activity of Complement Factor D in Complex with COMPOUND2

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

Protein crystallography data

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

Fluorine Binding Sites:

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 5fbe

Go back to Fluorine Binding Sites List in 5fbe
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 5fbe

Go back to Fluorine Binding Sites List in 5fbe
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 5fbe

Go back to Fluorine Binding Sites List in 5fbe
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

Reference:

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
Page generated: Thu Aug 1 09:19:53 2024

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