Fluorine in PDB 6w2j: CPS1 Bound to Allosteric Inhibitor H3B-374

All present enzymatic activity of CPS1 Bound to Allosteric Inhibitor H3B-374:
6.3.4.16;

The structure of CPS1 Bound to Allosteric Inhibitor H3B-374, PDB code: 6w2j was solved by N.A.Larsen, T.V.Nguyen, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	58.96 / 2.62
Space group	P 1
Cell size a, b, c (Å), α, β, γ (°)	71.66, 98.53, 142.53, 102.13, 97.94, 106.11
R / Rfree (%)	19 / 25

The structure of CPS1 Bound to Allosteric Inhibitor H3B-374 also contains other interesting chemical elements:

Zinc

(Zn)

2 atoms

The binding sites of Fluorine atom in the CPS1 Bound to Allosteric Inhibitor H3B-374 (pdb code 6w2j). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 4 binding sites of Fluorine where determined in the CPS1 Bound to Allosteric Inhibitor H3B-374, PDB code: 6w2j:
Jump to Fluorine binding site number: 1; 2; 3; 4;

Fluorine binding site 1 out of 4 in the CPS1 Bound to Allosteric Inhibitor H3B-374


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of CPS1 Bound to Allosteric Inhibitor H3B-374 within 5.0Å range: probe atom residue distance (Å) B Occ A:F1601 b:44.6 occ:1.00 F1 A:3741601 0.0 44.6 1.0 C20 A:3741601 1.3 43.7 1.0 C14 A:3741601 2.4 45.2 1.0 C19 A:3741601 2.4 41.5 1.0 C13 A:3741601 2.8 47.7 1.0 CB A:SER848 3.2 47.1 1.0 N2 A:3741601 3.2 44.2 1.0 C10 A:3741601 3.3 44.5 1.0 O3 A:3741601 3.5 48.5 1.0 CE3 A:TRP776 3.5 44.2 1.0 C15 A:3741601 3.6 43.5 1.0 C17 A:3741601 3.6 44.8 1.0 CB A:TRP776 3.9 45.7 1.0 CB A:LEU778 3.9 60.3 1.0 CA A:SER848 4.0 45.2 1.0 C16 A:3741601 4.1 46.8 1.0 CD2 A:TRP776 4.2 43.3 1.0 C12 A:3741601 4.2 42.1 1.0 CD2 A:LEU778 4.2 69.2 1.0 C9 A:3741601 4.3 42.5 1.0 C8 A:3741601 4.3 41.6 1.0 CG A:TRP776 4.3 45.1 1.0 CZ3 A:TRP776 4.4 48.1 1.0 OG A:SER848 4.4 46.9 1.0 C11 A:3741601 4.5 46.5 1.0 O A:SER848 4.5 47.3 1.0 CG A:LEU778 4.7 66.1 1.0 O4 A:3741601 4.7 45.9 1.0 C A:SER848 4.8 43.4 1.0 CA A:TRP776 4.9 46.3 1.0 O A:LEU778 4.9 61.7 1.0 CA A:LEU778 4.9 59.0 1.0 N A:TRP776 4.9 46.1 1.0 O A:ARG780 5.0 56.2 1.0

Fluorine binding site 2 out of 4 in the CPS1 Bound to Allosteric Inhibitor H3B-374


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of CPS1 Bound to Allosteric Inhibitor H3B-374 within 5.0Å range: probe atom residue distance (Å) B Occ A:F1601 b:38.1 occ:1.00 F2 A:3741601 0.0 38.1 1.0 C21 A:3741601 1.4 38.8 1.0 C22 A:3741601 2.4 41.0 1.0 C5 A:3741601 2.5 37.5 1.0 CD2 A:LEU813 3.0 38.7 1.0 C6 A:3741601 3.0 42.3 1.0 C7 A:3741601 3.1 42.8 1.0 N1 A:3741601 3.2 42.5 1.0 CG2 A:ILE851 3.6 43.3 1.0 C2 A:3741601 3.7 43.4 1.0 C4 A:3741601 3.7 37.6 1.0 O2 A:3741601 3.9 44.8 1.0 CB A:ILE851 3.9 42.6 1.0 CG2 A:ILE773 4.1 42.4 1.0 CD1 A:ILE773 4.1 43.1 1.0 C3 A:3741601 4.2 42.6 1.0 C11 A:3741601 4.4 46.5 1.0 C12 A:3741601 4.4 42.1 1.0 CG A:LEU813 4.4 40.9 1.0 C8 A:3741601 4.4 41.6 1.0 CG1 A:ILE851 4.4 44.3 1.0 O1 A:3741601 4.7 43.2 1.0 CG1 A:ILE773 4.8 43.0 1.0 C10 A:3741601 4.8 44.5 1.0

Fluorine binding site 3 out of 4 in the CPS1 Bound to Allosteric Inhibitor H3B-374


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of CPS1 Bound to Allosteric Inhibitor H3B-374 within 5.0Å range: probe atom residue distance (Å) B Occ B:F1601 b:46.7 occ:1.00 F1 B:3741601 0.0 46.7 1.0 C20 B:3741601 1.2 42.0 1.0 C14 B:3741601 2.2 43.1 1.0 C19 B:3741601 2.2 41.0 1.0 C13 B:3741601 2.7 43.3 1.0 N2 B:3741601 3.1 43.8 1.0 C10 B:3741601 3.3 43.5 1.0 O3 B:3741601 3.3 43.3 1.0 CB B:SER848 3.5 49.8 1.0 C15 B:3741601 3.5 45.1 1.0 C17 B:3741601 3.5 44.5 1.0 CE3 B:TRP776 3.6 47.3 1.0 CB B:LEU778 3.7 20.0 1.0 CD1 B:LEU778 3.9 20.0 1.0 CB B:TRP776 4.0 50.8 1.0 C16 B:3741601 4.0 44.8 1.0 CA B:SER848 4.1 50.8 1.0 C9 B:3741601 4.2 42.1 1.0 C12 B:3741601 4.2 42.0 1.0 CD2 B:TRP776 4.2 49.4 1.0 C8 B:3741601 4.2 45.4 1.0 CG B:LEU778 4.3 20.0 1.0 OG B:SER848 4.4 48.2 1.0 CZ3 B:TRP776 4.4 47.2 1.0 CG B:TRP776 4.4 51.0 1.0 O B:SER848 4.5 48.2 1.0 C11 B:3741601 4.5 42.7 1.0 O4 B:3741601 4.6 43.9 1.0 O B:LEU778 4.6 63.3 1.0 CA B:LEU778 4.7 60.9 1.0 O B:ARG780 4.8 69.1 1.0 C B:SER848 4.8 49.3 1.0 N B:TRP776 4.9 46.1 1.0 C B:LEU778 4.9 58.1 1.0 CA B:TRP776 4.9 49.1 1.0 N B:LEU778 5.0 60.6 1.0

Fluorine binding site 4 out of 4 in the CPS1 Bound to Allosteric Inhibitor H3B-374


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 4 of CPS1 Bound to Allosteric Inhibitor H3B-374 within 5.0Å range: probe atom residue distance (Å) B Occ B:F1601 b:47.3 occ:1.00 F2 B:3741601 0.0 47.3 1.0 C21 B:3741601 1.4 46.6 1.0 C22 B:3741601 2.3 46.2 1.0 C5 B:3741601 2.5 45.5 1.0 C6 B:3741601 3.0 45.8 1.0 C7 B:3741601 3.0 46.1 1.0 CD2 B:LEU813 3.0 48.5 1.0 N1 B:3741601 3.1 43.3 1.0 C2 B:3741601 3.6 46.8 1.0 CG2 B:ILE851 3.6 38.6 1.0 C4 B:3741601 3.7 44.7 1.0 O2 B:3741601 3.9 43.5 1.0 CD1 B:ILE773 4.0 49.1 1.0 CB B:ILE851 4.0 41.2 1.0 CG2 B:ILE773 4.0 43.3 1.0 C3 B:3741601 4.1 48.5 1.0 C11 B:3741601 4.3 42.7 1.0 C12 B:3741601 4.3 42.0 1.0 C8 B:3741601 4.5 45.4 1.0 CG B:LEU813 4.5 48.9 1.0 CG1 B:ILE851 4.5 40.5 1.0 O1 B:3741601 4.6 46.5 1.0 C10 B:3741601 4.8 43.5 1.0 CG1 B:ILE773 4.8 47.3 1.0

A.Rolfe, S.Yao, T.V.Nguyen, K.Omoto, F.Colombo, M.Virrankoski, F.H.Vaillancourt, L.Yu, A.Cook, D.Reynolds, S.Ioannidis, P.Zhu, N.A.Larsen, D.M.Bolduc. Discovery of 2,6-Dimethylpiperazines As Allosteric Inhibitors of CPS1. Acs Med.Chem.Lett. V. 11 1305 2020.
ISSN: ISSN 1948-5875
PubMed: 32551016
DOI: 10.1021/ACSMEDCHEMLETT.0C00145