Chlorine in PDB 6vn6: USP7 in Complex with Ligand Compound 14

Enzymatic activity of USP7 in Complex with Ligand Compound 14

All present enzymatic activity of USP7 in Complex with Ligand Compound 14:
3.4.19.12;

Protein crystallography data

The structure of USP7 in Complex with Ligand Compound 14, PDB code: 6vn6 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) 47.90 / 2.99
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 70.301, 65.680, 85.313, 90.00, 94.04, 90.00
R / Rfree (%) 21.9 / 26.7

Other elements in 6vn6:

The structure of USP7 in Complex with Ligand Compound 14 also contains other interesting chemical elements:

Zinc (Zn) 2 atoms

Chlorine Binding Sites:

The binding sites of Chlorine atom in the USP7 in Complex with Ligand Compound 14 (pdb code 6vn6). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 4 binding sites of Chlorine where determined in the USP7 in Complex with Ligand Compound 14, PDB code: 6vn6:
Jump to Chlorine binding site number: 1; 2; 3; 4;

Chlorine binding site 1 out of 4 in 6vn6

Go back to Chlorine Binding Sites List in 6vn6
Chlorine binding site 1 out of 4 in the USP7 in Complex with Ligand Compound 14


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of USP7 in Complex with Ligand Compound 14 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl601

b:78.8
occ:1.00
CL1 A:R4J601 0.0 78.8 1.0
C2 A:R4J601 1.7 74.7 1.0
C3 A:R4J601 2.7 72.5 1.0
C26 A:R4J601 2.7 80.5 1.0
CB A:ARG408 3.7 84.5 1.0
CG A:ARG408 3.7 80.8 1.0
CB A:ASN512 3.9 0.9 1.0
CD A:LYS420 4.0 95.6 1.0
C4 A:R4J601 4.0 76.8 1.0
C25 A:R4J601 4.0 84.4 1.0
CB A:HIS456 4.0 90.4 1.0
CD A:ARG408 4.1 81.8 1.0
CB A:TYR514 4.3 69.8 1.0
O A:ASN512 4.3 86.2 1.0
ND1 A:HIS456 4.4 92.8 1.0
ND2 A:ASN512 4.5 0.3 1.0
CG A:LYS420 4.5 99.6 1.0
CG A:HIS456 4.5 91.1 1.0
C20 A:R4J601 4.5 84.5 1.0
CE1 A:PHE409 4.5 93.2 1.0
CG A:ASN512 4.7 0.4 1.0
C A:ASN512 4.9 87.9 1.0
NE A:ARG408 5.0 84.5 1.0
CD1 A:TYR514 5.0 74.4 1.0

Chlorine binding site 2 out of 4 in 6vn6

Go back to Chlorine Binding Sites List in 6vn6
Chlorine binding site 2 out of 4 in the USP7 in Complex with Ligand Compound 14


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of USP7 in Complex with Ligand Compound 14 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl601

b:76.7
occ:1.00
CL19 A:R4J601 0.0 76.7 1.0
C18 A:R4J601 1.8 73.7 1.0
C14 A:R4J601 2.8 70.6 1.0
O15 A:R4J601 3.1 68.3 1.0
C16 A:R4J601 3.2 68.3 1.0
CG A:MET407 3.4 90.0 1.0
O17 A:R4J601 3.5 70.5 1.0
CG A:GLN351 3.5 67.6 1.0
CB A:GLN351 3.7 67.8 1.0
CA A:MET407 3.8 85.2 1.0
O A:LEU406 3.9 81.8 1.0
C A:LEU406 4.0 80.7 1.0
N A:MET407 4.0 83.1 1.0
CB A:GLN405 4.0 76.4 1.0
C11 A:R4J601 4.1 76.4 1.0
NE2 A:GLN297 4.1 73.6 1.0
CB A:MET407 4.2 91.0 1.0
CA A:GLN351 4.3 61.8 1.0
C A:GLN405 4.4 75.9 1.0
N A:LEU406 4.4 73.8 1.0
O A:GLN405 4.5 74.5 1.0
CA A:LEU406 4.7 74.5 1.0
C10 A:R4J601 4.8 79.4 1.0
CA A:GLN405 4.9 72.6 1.0
SD A:MET407 4.9 93.5 1.0
OE1 A:GLN297 4.9 74.1 1.0
C A:GLN351 4.9 60.5 1.0
CD A:GLN297 4.9 74.3 1.0

Chlorine binding site 3 out of 4 in 6vn6

Go back to Chlorine Binding Sites List in 6vn6
Chlorine binding site 3 out of 4 in the USP7 in Complex with Ligand Compound 14


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 3 of USP7 in Complex with Ligand Compound 14 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl601

b:0.0
occ:1.00
CL1 B:R4J601 0.0 0.0 1.0
C2 B:R4J601 1.7 0.6 1.0
C3 B:R4J601 2.7 0.2 1.0
C26 B:R4J601 2.7 0.3 1.0
CB B:ASN512 3.8 0.4 1.0
CG B:ARG408 3.8 1.0 1.0
CB B:ARG408 3.8 0.3 1.0
C4 B:R4J601 4.0 0.5 1.0
C25 B:R4J601 4.0 0.4 1.0
CD B:LYS420 4.0 0.8 1.0
CB B:HIS456 4.0 0.4 1.0
CD B:ARG408 4.2 0.6 1.0
ND1 B:HIS456 4.3 0.3 1.0
ND2 B:ASN512 4.3 0.6 1.0
O B:ASN512 4.3 0.7 1.0
CG B:HIS456 4.5 0.4 1.0
CB B:TYR514 4.5 95.7 1.0
C20 B:R4J601 4.5 1.0 1.0
CG B:ASN512 4.6 0.4 1.0
CG B:LYS420 4.6 0.6 1.0
CE1 B:PHE409 4.8 0.1 1.0
C B:ASN512 4.9 0.8 1.0
CA B:ASN512 4.9 0.9 1.0

Chlorine binding site 4 out of 4 in 6vn6

Go back to Chlorine Binding Sites List in 6vn6
Chlorine binding site 4 out of 4 in the USP7 in Complex with Ligand Compound 14


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 4 of USP7 in Complex with Ligand Compound 14 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl601

b:95.7
occ:1.00
CL19 B:R4J601 0.0 95.7 1.0
C18 B:R4J601 1.8 87.7 1.0
C14 B:R4J601 2.8 86.0 1.0
O15 B:R4J601 3.0 85.4 1.0
C16 B:R4J601 3.3 87.5 1.0
CG B:MET407 3.4 0.8 1.0
CA B:MET407 3.6 99.9 1.0
CG B:GLN351 3.7 84.9 1.0
O B:LEU406 3.7 0.2 1.0
O17 B:R4J601 3.7 84.2 1.0
C B:LEU406 3.8 0.7 1.0
N B:MET407 3.8 0.2 1.0
CB B:GLN351 3.8 87.0 1.0
CB B:GLN405 3.9 84.2 1.0
CB B:MET407 4.1 0.6 1.0
C11 B:R4J601 4.1 91.4 1.0
N B:LEU406 4.3 90.7 1.0
C B:GLN405 4.3 89.6 1.0
NE2 B:GLN297 4.3 92.4 1.0
CA B:GLN351 4.4 84.9 1.0
O B:GLN405 4.4 97.8 1.0
CA B:LEU406 4.6 95.2 1.0
C10 B:R4J601 4.8 90.6 1.0
CA B:GLN405 4.8 83.5 1.0
C B:MET407 4.9 0.1 1.0
SD B:MET407 5.0 0.8 1.0
C B:GLN351 5.0 86.8 1.0

Reference:

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
Page generated: Sat Dec 12 14:22:38 2020

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