Chlorine in PDB 8hje: Vismodegib Binds to the Catalytical Domain of Human Ubiquitin-Specific Protease 28

All present enzymatic activity of Vismodegib Binds to the Catalytical Domain of Human Ubiquitin-Specific Protease 28:
3.4.19.12;

The structure of Vismodegib Binds to the Catalytical Domain of Human Ubiquitin-Specific Protease 28, PDB code: 8hje was solved by L.Shi, H.Wang, Z.Xu, B.Xiong, N.Zhang, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	43.85 / 2.85
Space group	H 3 2
Cell size a, b, c (Å), α, β, γ (°)	105.099, 105.099, 327.422, 90, 90, 120
R / Rfree (%)	22.2 / 25.4

The binding sites of Chlorine atom in the Vismodegib Binds to the Catalytical Domain of Human Ubiquitin-Specific Protease 28 (pdb code 8hje). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 2 binding sites of Chlorine where determined in the Vismodegib Binds to the Catalytical Domain of Human Ubiquitin-Specific Protease 28, PDB code: 8hje:
Jump to Chlorine binding site number: 1; 2;

Chlorine binding site 1 out of 2 in the Vismodegib Binds to the Catalytical Domain of Human Ubiquitin-Specific Protease 28


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of Vismodegib Binds to the Catalytical Domain of Human Ubiquitin-Specific Protease 28 within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl801 b:92.7 occ:1.00 CL1 A:VIS801 0.0 92.7 1.0 C11 A:VIS801 1.8 99.6 1.0 C10 A:VIS801 2.7 110.5 1.0 C12 A:VIS801 2.8 83.1 1.0 C15 A:VIS801 3.0 79.8 1.0 C14 A:VIS801 3.1 71.1 1.0 OE1 A:GLN315 3.8 76.7 1.0 N A:GLN315 4.0 61.0 1.0 C9 A:VIS801 4.0 91.0 1.0 CD1 A:LEU264 4.1 107.4 1.0 C13 A:VIS801 4.1 75.2 1.0 C16 A:VIS801 4.1 98.9 1.0 CB A:GLN315 4.1 67.8 1.0 N1 A:VIS801 4.3 72.1 1.0 CD2 A:LEU264 4.5 113.2 1.0 CA A:GLN315 4.5 64.3 1.0 C8 A:VIS801 4.5 79.8 1.0 CD A:GLN315 4.6 88.7 1.0 CG A:LEU264 4.6 108.7 1.0 CB A:LEU264 4.7 100.5 1.0 C A:GLY314 4.8 59.2 1.0 CG2 A:THR364 4.9 51.5 1.0

Chlorine binding site 2 out of 2 in the Vismodegib Binds to the Catalytical Domain of Human Ubiquitin-Specific Protease 28


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of Vismodegib Binds to the Catalytical Domain of Human Ubiquitin-Specific Protease 28 within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl801 b:98.5 occ:1.00 CL A:VIS801 0.0 98.5 1.0 C5 A:VIS801 1.7 92.8 1.0 C6 A:VIS801 2.7 92.4 1.0 C4 A:VIS801 2.7 87.2 1.0 C7 A:VIS801 3.0 85.4 1.0 O A:SER257 3.2 98.5 1.0 O2 A:VIS801 3.2 104.2 1.0 CA A:SER257 3.4 96.2 1.0 CE1 A:HIS261 3.4 90.6 1.0 CB A:THR260 3.6 65.9 1.0 OE1 A:GLU366 3.7 74.9 1.0 C A:SER257 3.7 101.5 1.0 CG2 A:THR260 3.8 63.5 1.0 NE2 A:HIS261 3.9 87.2 1.0 ND1 A:HIS261 3.9 89.2 1.0 CB A:SER257 4.0 84.9 1.0 C3 A:VIS801 4.0 86.0 1.0 C9 A:VIS801 4.0 91.0 1.0 C1 A:VIS801 4.0 97.3 1.0 N A:VIS801 4.0 80.0 1.0 OG1 A:THR260 4.0 69.1 1.0 C8 A:VIS801 4.3 79.8 1.0 O A:VAL256 4.3 112.8 1.0 N A:SER257 4.5 95.7 1.0 C2 A:VIS801 4.5 89.3 1.0 CD2 A:HIS261 4.6 88.5 1.0 CG A:HIS261 4.6 91.3 1.0 CD A:GLU366 4.8 78.7 1.0 C A:VAL256 4.9 110.9 1.0 CA A:THR260 4.9 72.5 1.0 C10 A:VIS801 5.0 110.5 1.0 N A:HIS261 5.0 76.0 1.0

D.Zhou, Z.Xu, Y.Huang, H.Wang, X.Zhu, W.Zhang, W.Song, T.Gao, T.Liu, M.Wang, L.Shi, N.Zhang, B.Xiong. Structure-Based Discovery of Potent USP28 Inhibitors Derived From Vismodegib. Eur.J.Med.Chem. V. 254 15369 2023.
ISSN: ISSN 0223-5234
PubMed: 37075624
DOI: 10.1016/J.EJMECH.2023.115369