Fluorine in PDB 6rfw: Crystal Structure of T. Brucei Pde-B1 Catalytic Domain with Inhibitor Npd-1039

The structure of Crystal Structure of T. Brucei Pde-B1 Catalytic Domain with Inhibitor Npd-1039, PDB code: 6rfw was solved by A.K.Singh, D.G.Brown, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	65.11 / 2.18
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	113.716, 116.553, 68.525, 90.00, 108.17, 90.00
R / Rfree (%)	17.5 / 23.4

The structure of Crystal Structure of T. Brucei Pde-B1 Catalytic Domain with Inhibitor Npd-1039 also contains other interesting chemical elements:

Magnesium	(Mg)	2 atoms
Zinc	(Zn)	2 atoms

The binding sites of Fluorine atom in the Crystal Structure of T. Brucei Pde-B1 Catalytic Domain with Inhibitor Npd-1039 (pdb code 6rfw). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 2 binding sites of Fluorine where determined in the Crystal Structure of T. Brucei Pde-B1 Catalytic Domain with Inhibitor Npd-1039, PDB code: 6rfw:
Jump to Fluorine binding site number: 1; 2;

Fluorine binding site 1 out of 2 in the Crystal Structure of T. Brucei Pde-B1 Catalytic Domain with Inhibitor Npd-1039


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of Crystal Structure of T. Brucei Pde-B1 Catalytic Domain with Inhibitor Npd-1039 within 5.0Å range: probe atom residue distance (Å) B Occ A:F1007 b:0.5 occ:1.00 F1 A:K1Q1007 0.0 0.5 1.0 C25 A:K1Q1007 1.4 0.6 1.0 C26 A:K1Q1007 2.3 85.1 1.0 C24 A:K1Q1007 2.4 97.3 1.0 C23 A:K1Q1007 2.9 87.3 1.0 C22 A:K1Q1007 3.3 81.0 1.0 C27 A:K1Q1007 3.6 83.3 1.0 SD A:MET861 3.6 95.6 1.0 C29 A:K1Q1007 3.6 89.6 1.0 C10 A:K1Q1007 3.8 83.3 1.0 C11 A:K1Q1007 4.0 68.4 1.0 CE A:MET861 4.0 86.7 1.0 C28 A:K1Q1007 4.1 92.1 1.0 C4 A:K1Q1007 4.1 73.1 1.0 CD1 A:PHE877 4.2 54.7 1.0 N1 A:K1Q1007 4.2 80.9 1.0 C19 A:K1Q1007 4.3 78.4 1.0 N3 A:K1Q1007 4.4 76.3 1.0 C9 A:K1Q1007 4.4 76.3 1.0 C20 A:K1Q1007 4.5 78.2 1.0 C3 A:K1Q1007 4.7 81.0 1.0 CE2 A:PHE844 4.8 76.6 1.0 CE1 A:PHE877 4.8 56.8 1.0 N2 A:K1Q1007 4.8 74.4 1.0 C21 A:K1Q1007 5.0 82.7 1.0

Fluorine binding site 2 out of 2 in the Crystal Structure of T. Brucei Pde-B1 Catalytic Domain with Inhibitor Npd-1039


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of Crystal Structure of T. Brucei Pde-B1 Catalytic Domain with Inhibitor Npd-1039 within 5.0Å range: probe atom residue distance (Å) B Occ B:F1007 b:94.9 occ:1.00 F1 B:K1Q1007 0.0 94.9 1.0 C25 B:K1Q1007 1.4 0.8 1.0 C26 B:K1Q1007 2.3 99.6 1.0 C24 B:K1Q1007 2.4 0.6 1.0 C22 B:K1Q1007 2.8 92.8 1.0 C23 B:K1Q1007 2.9 95.6 1.0 CD1 B:PHE877 3.6 46.6 1.0 C27 B:K1Q1007 3.6 96.8 1.0 C29 B:K1Q1007 3.6 0.3 1.0 C11 B:K1Q1007 3.8 56.3 1.0 CE B:MET861 4.0 91.7 1.0 C28 B:K1Q1007 4.1 98.3 1.0 SD B:MET861 4.2 89.7 1.0 C10 B:K1Q1007 4.2 63.6 1.0 N3 B:K1Q1007 4.2 73.7 1.0 C4 B:K1Q1007 4.2 58.6 1.0 N1 B:K1Q1007 4.3 60.4 1.0 CE1 B:PHE877 4.3 48.1 1.0 CG B:PHE877 4.4 43.9 1.0 C20 B:K1Q1007 4.4 58.3 1.0 CB B:PHE877 4.4 44.7 1.0 C19 B:K1Q1007 4.4 61.4 1.0 C9 B:K1Q1007 4.4 64.2 1.0 C3 B:K1Q1007 4.8 63.2 1.0 C21 B:K1Q1007 4.8 62.4 1.0 CA B:PHE877 4.8 48.5 1.0 N2 B:K1Q1007 4.9 68.9 1.0

E.De Heuvel, A.K.Singh, P.Boronat, A.J.Kooistra, T.Van Der Meer, P.Sadek, A.R.Blaazer, N.C.Shaner, D.S.Bindels, G.Caljon, L.Maes, G.J.Sterk, M.Siderius, M.Oberholzer, I.J.P.De Esch, D.G.Brown, R.Leurs. Alkynamide Phthalazinones As A New Class of TBRPDEB1 Inhibitors (Part 2). Bioorg.Med.Chem. V. 27 4013 2019.
ISSN: ESSN 1464-3391
PubMed: 31378593
DOI: 10.1016/J.BMC.2019.06.026