Fluorine in PDB 6vn3: USP7 in Complex with Ligand Compound 23

All present enzymatic activity of USP7 in Complex with Ligand Compound 23:
3.4.19.12;

The structure of USP7 in Complex with Ligand Compound 23, PDB code: 6vn3 was solved by P.R.Leger, D.J.Wustrow, D.X.Hu, S.Krapp, K.Maskos, M.Blaesse, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	48.05 / 2.73
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	70.510, 65.834, 85.077, 90.00, 94.62, 90.00
R / Rfree (%)	22.2 / 29

The structure of USP7 in Complex with Ligand Compound 23 also contains other interesting chemical elements:

Chlorine

(Cl)

2 atoms

The binding sites of Fluorine atom in the USP7 in Complex with Ligand Compound 23 (pdb code 6vn3). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 2 binding sites of Fluorine where determined in the USP7 in Complex with Ligand Compound 23, PDB code: 6vn3:
Jump to Fluorine binding site number: 1; 2;

Fluorine binding site 1 out of 2 in the USP7 in Complex with Ligand Compound 23


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of USP7 in Complex with Ligand Compound 23 within 5.0Å range: probe atom residue distance (Å) B Occ A:F601 b:73.6 occ:1.00 F16 A:R3Y601 0.0 73.6 1.0 C14 A:R3Y601 1.4 65.3 1.0 C13 A:R3Y601 2.4 56.7 1.0 C9 A:R3Y601 2.5 56.6 1.0 C11 A:R3Y601 2.8 55.5 1.0 N12 A:R3Y601 2.9 49.4 1.0 O8 A:R3Y601 3.0 56.9 1.0 CE A:MET292 3.2 1.0 1.0 C1 A:R3Y601 3.6 67.5 1.0 O A:MET292 3.7 0.4 1.0 C7 A:R3Y601 3.9 56.5 1.0 C2 A:R3Y601 4.2 65.0 1.0 CZ A:PHE409 4.5 81.9 1.0 C A:MET292 4.6 0.4 1.0 CE2 A:PHE409 4.7 79.8 1.0 ND1 A:HIS461 4.8 0.1 0.0 CA A:MET292 4.8 97.7 1.0 CB A:MET292 4.9 0.6 1.0 SD A:MET292 4.9 0.6 1.0

Fluorine binding site 2 out of 2 in the USP7 in Complex with Ligand Compound 23


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of USP7 in Complex with Ligand Compound 23 within 5.0Å range: probe atom residue distance (Å) B Occ B:F601 b:85.0 occ:1.00 F16 B:R3Y601 0.0 85.0 1.0 C14 B:R3Y601 1.4 77.0 1.0 C13 B:R3Y601 2.4 70.8 1.0 C9 B:R3Y601 2.5 63.4 1.0 O8 B:R3Y601 2.9 60.1 1.0 C11 B:R3Y601 3.0 68.1 1.0 N12 B:R3Y601 3.1 71.6 1.0 CE B:MET292 3.2 95.9 1.0 C1 B:R3Y601 3.6 60.1 1.0 C7 B:R3Y601 3.8 55.6 1.0 O B:MET292 4.0 75.2 1.0 C2 B:R3Y601 4.1 57.9 1.0 CZ B:PHE409 4.4 95.0 1.0 CE2 B:PHE409 4.6 96.5 1.0 ND1 B:HIS461 4.6 0.4 0.0 N B:HIS461 4.7 0.2 1.0 SD B:MET292 4.9 0.1 1.0 C B:MET292 5.0 81.9 1.0 CE1 B:HIS461 5.0 0.8 0.0

P.R.Leger, D.X.Hu, B.Biannic, M.Bui, X.Han, E.Karbarz, J.Maung, A.Okano, M.Osipov, G.M.Shibuya, K.Young, C.Higgs, B.Abraham, D.Bradford, C.Cho, C.Colas, S.Jacobson, Y.M.Ohol, D.Pookot, P.Rana, J.Sanchez, N.Shah, M.Sun, S.Wong, D.G.Brockstedt, P.D.Kassner, J.B.Schwarz, D.J.Wustrow. Discovery of Potent, Selective, and Orally Bioavailable Inhibitors of USP7 with in Vivo Anti-Tumor Activity. J.Med.Chem. 2020.
ISSN: ISSN 0022-2623
PubMed: 32302140
DOI: 10.1021/ACS.JMEDCHEM.0C00245