Fluorine in PDB 8wsm: NLRP3 Nacht Domain in Complex with Compound 32

The structure of NLRP3 Nacht Domain in Complex with Compound 32, PDB code: 8wsm was solved by S.Akai, T.Orita, T.Adachi, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	84.00 / 2.70
Space group	P 61 2 2
Cell size a, b, c (Å), α, β, γ (°)	96.997, 96.997, 266.057, 90, 90, 120
R / Rfree (%)	21.3 / 24.8

The structure of NLRP3 Nacht Domain in Complex with Compound 32 also contains other interesting chemical elements:

Magnesium

(Mg)

1 atom

The binding sites of Fluorine atom in the NLRP3 Nacht Domain in Complex with Compound 32 (pdb code 8wsm). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 3 binding sites of Fluorine where determined in the NLRP3 Nacht Domain in Complex with Compound 32, PDB code: 8wsm:
Jump to Fluorine binding site number: 1; 2; 3;

Fluorine binding site 1 out of 3 in the NLRP3 Nacht Domain in Complex with Compound 32


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of NLRP3 Nacht Domain in Complex with Compound 32 within 5.0Å range: probe atom residue distance (Å) B Occ A:F703 b:61.1 occ:1.00 F A:XE3703 0.0 61.1 1.0 C10 A:XE3703 1.3 62.3 1.0 F2 A:XE3703 2.1 69.3 1.0 F1 A:XE3703 2.2 67.0 1.0 C6 A:XE3703 2.3 61.0 1.0 C5 A:XE3703 2.8 57.4 1.0 CE1 A:TYR632 3.4 52.7 1.0 CG A:MET661 3.5 63.1 1.0 C7 A:XE3703 3.6 61.4 1.0 C4 A:XE3703 4.2 60.1 1.0 CD1 A:TYR632 4.2 53.2 1.0 NH1 A:ARG578 4.2 52.4 1.0 CZ A:TYR632 4.2 53.9 1.0 OH A:TYR632 4.3 52.4 1.0 O1 A:XE3703 4.5 60.3 1.0 CB A:MET661 4.5 59.3 1.0 SD A:MET661 4.5 74.2 1.0 C8 A:XE3703 4.7 59.9 1.0 OG1 A:THR439 4.7 63.6 1.0 CE A:MET661 5.0 65.7 1.0 C9 A:XE3703 5.0 62.2 1.0

Fluorine binding site 2 out of 3 in the NLRP3 Nacht Domain in Complex with Compound 32


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of NLRP3 Nacht Domain in Complex with Compound 32 within 5.0Å range: probe atom residue distance (Å) B Occ A:F703 b:67.0 occ:1.00 F1 A:XE3703 0.0 67.0 1.0 C10 A:XE3703 1.3 62.3 1.0 F A:XE3703 2.2 61.1 1.0 F2 A:XE3703 2.2 69.3 1.0 C6 A:XE3703 2.3 61.0 1.0 C5 A:XE3703 3.1 57.4 1.0 C7 A:XE3703 3.2 61.4 1.0 CG A:MET408 3.4 62.9 1.0 CG A:MET661 3.6 63.1 1.0 CE1 A:PHE410 3.7 60.8 1.0 CE A:MET661 3.9 65.7 1.0 CG1 A:ILE411 4.2 58.9 1.0 CA A:MET408 4.2 60.0 1.0 SD A:MET661 4.3 74.2 1.0 CB A:MET661 4.3 59.3 1.0 CB A:MET408 4.3 59.7 1.0 CZ A:PHE410 4.3 58.0 1.0 C4 A:XE3703 4.4 60.1 1.0 C8 A:XE3703 4.4 59.9 1.0 O A:MET408 4.5 58.8 1.0 SD A:MET408 4.6 77.8 1.0 CD1 A:PHE410 4.6 62.2 1.0 CD1 A:ILE411 4.9 60.5 1.0 C A:MET408 4.9 62.0 1.0 C9 A:XE3703 4.9 62.2 1.0

Fluorine binding site 3 out of 3 in the NLRP3 Nacht Domain in Complex with Compound 32


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of NLRP3 Nacht Domain in Complex with Compound 32 within 5.0Å range: probe atom residue distance (Å) B Occ A:F703 b:69.3 occ:1.00 F2 A:XE3703 0.0 69.3 1.0 C10 A:XE3703 1.3 62.3 1.0 F A:XE3703 2.1 61.1 1.0 F1 A:XE3703 2.2 67.0 1.0 C6 A:XE3703 2.4 61.0 1.0 C7 A:XE3703 2.8 61.4 1.0 OG1 A:THR439 3.1 63.6 1.0 CG A:MET408 3.6 62.9 1.0 C5 A:XE3703 3.6 57.4 1.0 SD A:MET408 3.8 77.8 1.0 CG A:MET661 3.9 63.1 1.0 SD A:MET661 4.0 74.2 1.0 CE A:MET408 4.1 53.5 1.0 C8 A:XE3703 4.1 59.9 1.0 CE A:MET661 4.2 65.7 1.0 CB A:THR439 4.5 64.9 1.0 CB A:MET408 4.6 59.7 1.0 CE1 A:TYR632 4.7 52.7 1.0 C4 A:XE3703 4.8 60.1 1.0 C9 A:XE3703 5.0 62.2 1.0 CG2 A:THR439 5.0 62.2 1.0

Y.Ohba, K.Adachi, T.Furukawa, T.Nishimaru, K.Sakurai, R.Masuo, T.Inami, T.Orita, S.Akai, T.Adachi, K.Usui, Y.Hamada, M.Mori, T.Kurimoto, T.Wakashima, Y.Akiyama, S.Miyazaki, S.Noji. Discovery of Novel NLRP3 Inflammasome Inhibitors Composed of An Oxazole Scaffold Bearing An Acylsulfamide. Acs Med.Chem.Lett. 2023.
ISSN: ISSN 1948-5875
DOI: 10.1021/ACSMEDCHEMLETT.3C00433