Fluorine in PDB 6zvl: ARUK3000263 Complex with Notum

All present enzymatic activity of ARUK3000263 Complex with Notum:
3.1.1.98;

The structure of ARUK3000263 Complex with Notum, PDB code: 6zvl was solved by Y.Zhao, R.Ruza, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	52.83 / 1.30
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	59.805, 71.791, 78.036, 90.00, 90.00, 90.00
R / Rfree (%)	20.1 / 22.3

The structure of ARUK3000263 Complex with Notum also contains other interesting chemical elements:

Chlorine

(Cl)

1 atom

The binding sites of Fluorine atom in the ARUK3000263 Complex with Notum (pdb code 6zvl). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 3 binding sites of Fluorine where determined in the ARUK3000263 Complex with Notum, PDB code: 6zvl:
Jump to Fluorine binding site number: 1; 2; 3;

Fluorine binding site 1 out of 3 in the ARUK3000263 Complex with Notum


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of ARUK3000263 Complex with Notum within 5.0Å range: probe atom residue distance (Å) B Occ A:F509 b:0.8 occ:1.00 F14 A:QR2509 0.0 0.8 1.0 C13 A:QR2509 1.4 50.9 1.0 F15 A:QR2509 2.0 0.8 1.0 C12 A:QR2509 2.2 93.5 1.0 C17 A:QR2509 2.4 73.0 1.0 F16 A:QR2509 2.6 89.4 1.0 HG21 A:VAL187 2.7 15.9 1.0 HD11 A:ILE291 3.1 19.5 0.6 HE1 A:TYR129 3.3 27.8 1.0 HG11 A:VAL187 3.4 23.3 1.0 C10 A:QR2509 3.5 33.2 1.0 CG2 A:VAL187 3.5 13.2 1.0 HG22 A:VAL187 3.5 15.9 1.0 HD2 A:PHE319 3.6 20.5 1.0 HG21 A:THR236 3.7 12.6 1.0 C01 A:QR2509 3.8 34.7 1.0 HD1 A:TYR129 3.8 23.0 1.0 HD11 A:ILE291 3.8 18.9 0.4 CE1 A:TYR129 3.9 23.2 1.0 HG13 A:VAL187 3.9 23.3 1.0 CD1 A:ILE291 4.0 16.2 0.6 CG1 A:VAL187 4.0 19.4 1.0 HG12 A:ILE291 4.1 30.6 0.4 HD12 A:ILE291 4.1 19.5 0.6 CD1 A:TYR129 4.1 19.1 1.0 HG23 A:VAL187 4.2 15.9 1.0 HG13 A:ILE291 4.3 29.8 0.6 HD13 A:ILE291 4.3 18.9 0.4 CB A:VAL187 4.3 12.8 1.0 CL1 A:QR2509 4.4 56.6 1.0 HB3 A:PHE319 4.4 15.7 1.0 HE2 A:PHE268 4.4 17.6 1.0 CD1 A:ILE291 4.4 15.8 0.4 OG1 A:THR236 4.5 11.5 1.0 HB A:THR236 4.5 13.3 1.0 C09 A:QR2509 4.5 25.1 1.0 CD2 A:PHE319 4.5 17.1 1.0 HD2 A:PHE268 4.6 15.7 1.0 HA A:ALA233 4.6 13.0 1.0 HD13 A:ILE291 4.6 19.5 0.6 CG2 A:THR236 4.6 10.4 1.0 O07 A:QR2509 4.6 33.1 1.0 CG1 A:ILE291 4.6 24.8 0.6 C08 A:QR2509 4.6 23.9 1.0 C02 A:QR2509 4.7 26.9 1.0 CG1 A:ILE291 4.7 25.5 0.4 HB A:VAL187 4.7 15.4 1.0 CB A:THR236 4.8 11.1 1.0 CZ A:TYR129 4.8 30.2 1.0 HG12 A:ILE291 4.9 29.8 0.6 HG12 A:VAL187 4.9 23.3 1.0 HG1 A:THR236 4.9 13.8 1.0 CE2 A:PHE268 4.9 14.7 1.0 HG13 A:ILE291 4.9 30.6 0.4 CD2 A:PHE268 5.0 13.1 1.0

Fluorine binding site 2 out of 3 in the ARUK3000263 Complex with Notum


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of ARUK3000263 Complex with Notum within 5.0Å range: probe atom residue distance (Å) B Occ A:F509 b:0.8 occ:1.00 F15 A:QR2509 0.0 0.8 1.0 C13 A:QR2509 1.4 50.9 1.0 F14 A:QR2509 2.0 0.8 1.0 F16 A:QR2509 2.0 89.4 1.0 HD13 A:ILE291 2.4 18.9 0.4 HD11 A:ILE291 2.4 18.9 0.4 HD11 A:ILE291 2.6 19.5 0.6 HG13 A:ILE291 2.7 29.8 0.6 CD1 A:ILE291 2.8 15.8 0.4 HD2 A:PHE319 2.8 20.5 1.0 C12 A:QR2509 2.8 93.5 1.0 HB3 A:PHE319 2.8 15.7 1.0 HG12 A:ILE291 3.0 30.6 0.4 CD1 A:ILE291 3.2 16.2 0.6 HD12 A:ILE291 3.3 19.5 0.6 CG1 A:ILE291 3.4 24.8 0.6 CG1 A:ILE291 3.4 25.5 0.4 CL1 A:QR2509 3.5 56.6 1.0 C10 A:QR2509 3.5 33.2 1.0 CD2 A:PHE319 3.5 17.1 1.0 HD12 A:ILE291 3.6 18.9 0.4 CB A:PHE319 3.6 13.1 1.0 HG21 A:THR236 3.7 12.6 1.0 HG21 A:VAL187 3.7 15.9 1.0 HG12 A:ILE291 3.8 29.8 0.6 C17 A:QR2509 3.8 73.0 1.0 HG13 A:ILE291 3.9 30.6 0.4 HB2 A:PHE319 3.9 15.7 1.0 HG11 A:VAL187 3.9 23.3 1.0 CG A:PHE319 4.0 12.8 1.0 HG21 A:ILE291 4.1 26.2 0.4 HG21 A:ILE291 4.1 27.6 0.6 HD13 A:ILE291 4.1 19.5 0.6 O A:PHE319 4.3 13.8 1.0 HE1 A:TYR129 4.5 27.8 1.0 CE2 A:PHE319 4.6 14.3 1.0 CB A:ILE291 4.6 29.6 0.6 HD2 A:PHE268 4.6 15.7 1.0 CG2 A:THR236 4.6 10.4 1.0 CB A:ILE291 4.7 14.5 0.4 CG2 A:VAL187 4.7 13.2 1.0 HE2 A:PHE319 4.7 17.1 1.0 CG2 A:ILE291 4.7 21.8 0.4 CG2 A:ILE291 4.7 23.0 0.6 HB3 A:PRO287 4.8 47.3 1.0 CA A:PHE319 4.8 11.4 1.0 CG1 A:VAL187 4.8 19.4 1.0 C A:PHE319 4.8 12.4 1.0 C09 A:QR2509 4.9 25.1 1.0 HG23 A:ILE291 4.9 26.2 0.4 HG23 A:ILE291 4.9 27.6 0.6 HG23 A:THR236 4.9 12.6 1.0 CE1 A:TYR129 5.0 23.2 1.0 HB A:ILE291 5.0 35.5 0.6

Fluorine binding site 3 out of 3 in the ARUK3000263 Complex with Notum


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of ARUK3000263 Complex with Notum within 5.0Å range: probe atom residue distance (Å) B Occ A:F509 b:89.4 occ:1.00 F16 A:QR2509 0.0 89.4 1.0 C13 A:QR2509 1.4 50.9 1.0 F15 A:QR2509 2.0 0.8 1.0 C12 A:QR2509 2.2 93.5 1.0 F14 A:QR2509 2.6 0.8 1.0 HD2 A:PHE268 2.6 15.7 1.0 C10 A:QR2509 2.8 33.2 1.0 CL1 A:QR2509 2.9 56.6 1.0 HG21 A:THR236 3.1 12.6 1.0 C17 A:QR2509 3.2 73.0 1.0 HB3 A:PHE319 3.3 15.7 1.0 CD2 A:PHE268 3.3 13.1 1.0 O A:PHE319 3.4 13.8 1.0 HB2 A:PHE268 3.7 15.6 1.0 HD11 A:ILE291 3.7 18.9 0.4 HG1 A:THR236 3.8 13.8 1.0 HE2 A:PHE268 3.8 17.6 1.0 HD13 A:ILE291 3.8 18.9 0.4 OG1 A:THR236 3.9 11.5 1.0 CG2 A:THR236 3.9 10.4 1.0 CE2 A:PHE268 4.0 14.7 1.0 HG23 A:THR236 4.0 12.6 1.0 HD2 A:PHE319 4.0 20.5 1.0 C09 A:QR2509 4.0 25.1 1.0 O A:HOH628 4.1 12.3 1.0 CG A:PHE268 4.3 12.6 1.0 CD1 A:ILE291 4.3 15.8 0.4 CB A:PHE319 4.3 13.1 1.0 C A:PHE319 4.3 12.4 1.0 C01 A:QR2509 4.4 34.7 1.0 HG13 A:ILE291 4.4 29.8 0.6 CB A:PHE268 4.4 13.0 1.0 CB A:THR236 4.5 11.1 1.0 HG11 A:VAL187 4.5 23.3 1.0 HD11 A:ILE291 4.6 19.5 0.6 HB2 A:PHE319 4.7 15.7 1.0 HG22 A:THR236 4.7 12.6 1.0 C08 A:QR2509 4.7 23.9 1.0 HB A:THR236 4.7 13.3 1.0 HA A:PHE320 4.8 14.9 1.0 HB3 A:PHE268 4.8 15.6 1.0 CD2 A:PHE319 4.8 17.1 1.0 CA A:PHE319 4.9 11.4 1.0 HD12 A:ILE291 4.9 18.9 0.4 HG21 A:VAL187 5.0 15.9 1.0 HG12 A:ILE291 5.0 30.6 0.4 CE1 A:PHE320 5.0 16.2 1.0

W.Mahy, N.J.Willis, Y.Zhao, H.L.Woodward, F.Svensson, J.Sipthorp, L.Vecchia, R.R.Ruza, J.Hillier, S.Kjaer, S.Frew, A.Monaghan, M.Bictash, P.C.Salinas, P.Whiting, J.P.Vincent, E.Y.Jones, P.V.Fish. 5-Phenyl-1,3,4-Oxadiazol-2(3 H )-Ones Are Potent Inhibitors of Notum Carboxylesterase Activity Identified By the Optimization of A Crystallographic Fragment Screening Hit. J.Med.Chem. V. 63 12942 2020.
ISSN: ISSN 0022-2623
PubMed: 33124429
DOI: 10.1021/ACS.JMEDCHEM.0C01391