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Fluorine in PDB 5n9t: Crystal Structure of USP7 in Complex with A Potent, Selective and Reversible Small-Molecule Inhibitor

Enzymatic activity of Crystal Structure of USP7 in Complex with A Potent, Selective and Reversible Small-Molecule Inhibitor

All present enzymatic activity of Crystal Structure of USP7 in Complex with A Potent, Selective and Reversible Small-Molecule Inhibitor:
3.4.19.12;

Protein crystallography data

The structure of Crystal Structure of USP7 in Complex with A Potent, Selective and Reversible Small-Molecule Inhibitor, PDB code: 5n9t was solved by T.Harrison, G.Gavory, C.O'dowd, M.Helm, J.Flasz, E.Arkoudis, A.Dossang, C.Hughes, E.Cassidy, K.Mcclelland, E.Odrzywol, N.Page, O.Barker, H.Miel, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 29.92 / 1.73
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 75.507, 67.623, 81.046, 90.00, 105.90, 90.00
R / Rfree (%) 16.1 / 22.4

Fluorine Binding Sites:

The binding sites of Fluorine atom in the Crystal Structure of USP7 in Complex with A Potent, Selective and Reversible Small-Molecule Inhibitor (pdb code 5n9t). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 6 binding sites of Fluorine where determined in the Crystal Structure of USP7 in Complex with A Potent, Selective and Reversible Small-Molecule Inhibitor, PDB code: 5n9t:
Jump to Fluorine binding site number: 1; 2; 3; 4; 5; 6;

Fluorine binding site 1 out of 6 in 5n9t

Go back to Fluorine Binding Sites List in 5n9t
Fluorine binding site 1 out of 6 in the Crystal Structure of USP7 in Complex with A Potent, Selective and Reversible Small-Molecule Inhibitor


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of Crystal Structure of USP7 in Complex with A Potent, Selective and Reversible Small-Molecule Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F1005

b:30.1
occ:1.00
 F2 A:8QQ1005 0.0 30.1 1.0
C17 A:8QQ1005 1.3 26.5 1.0
F A:8QQ1005 2.2 30.8 1.0
F1 A:8QQ1005 2.2 31.1 1.0
C15 A:8QQ1005 2.3 26.7 1.0
C16 A:8QQ1005 2.9 27.7 1.0
CE1 A:HIS456 3.2 27.5 1.0
N A:ASN460 3.3 31.8 1.0
C A:ASP459 3.5 34.2 1.0
C24 A:8QQ1005 3.5 27.4 1.0
CA A:ASN460 3.6 31.9 1.0
C14 A:8QQ1005 3.7 28.3 1.0
NE2 A:HIS456 3.7 28.6 1.0
O A:ASP459 3.7 31.2 1.0
C28 A:8QQ1005 3.7 29.4 1.0
C A:ASN460 3.8 29.0 1.0
O A:ASN460 3.8 32.5 1.0
ND1 A:HIS456 3.9 29.1 1.0
CD A:LYS420 3.9 30.3 1.0
CB A:LYS420 3.9 33.2 1.0
CA A:ASP459 4.2 30.2 1.0
CG A:LYS420 4.4 30.3 1.0
O A:GLY458 4.5 30.5 1.0
C25 A:8QQ1005 4.6 26.7 1.0
N A:HIS461 4.6 30.7 1.0
CD2 A:HIS456 4.6 27.5 1.0
O A:HOH1315 4.6 47.3 1.0
N A:ASP459 4.7 30.8 1.0
CG A:HIS456 4.7 27.1 1.0
C27 A:8QQ1005 4.8 27.5 1.0
O A:HOH1162 4.8 40.9 1.0
C A:GLY458 4.8 30.2 1.0
C13 A:8QQ1005 4.8 29.2 1.0

Fluorine binding site 2 out of 6 in 5n9t

Go back to Fluorine Binding Sites List in 5n9t
Fluorine binding site 2 out of 6 in the Crystal Structure of USP7 in Complex with A Potent, Selective and Reversible Small-Molecule Inhibitor


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of Crystal Structure of USP7 in Complex with A Potent, Selective and Reversible Small-Molecule Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F1005

b:30.8
occ:1.00
 F A:8QQ1005 0.0 30.8 1.0
C17 A:8QQ1005 1.3 26.5 1.0
F1 A:8QQ1005 2.1 31.1 1.0
F2 A:8QQ1005 2.2 30.1 1.0
C15 A:8QQ1005 2.4 26.7 1.0
C14 A:8QQ1005 2.9 28.3 1.0
CE1 A:PHE409 3.0 35.8 1.0
C16 A:8QQ1005 3.1 27.7 1.0
C24 A:8QQ1005 3.1 27.4 1.0
CZ A:PHE409 3.3 37.4 1.0
CD1 A:PHE409 3.4 31.8 1.0
O A:HOH1315 3.8 47.3 1.0
CE2 A:PHE409 4.0 38.5 1.0
CG A:PHE409 4.1 33.5 1.0
CB A:LYS420 4.2 33.2 1.0
O A:ASP459 4.3 31.2 1.0
CD2 A:PHE409 4.3 35.8 1.0
C13 A:8QQ1005 4.4 29.2 1.0
C25 A:8QQ1005 4.4 26.7 1.0
CA A:ASN460 4.4 31.9 1.0
C28 A:8QQ1005 4.4 29.4 1.0
CE1 A:HIS461 4.5 36.5 1.0
C A:ASP459 4.6 34.2 1.0
N A:ASN460 4.7 31.8 1.0
O A:HOH1162 4.7 40.9 1.0
ND1 A:HIS461 4.7 32.1 1.0
N A:LYS420 4.7 34.3 1.0
C A:ASN460 4.8 29.0 1.0
CA A:LYS420 4.9 33.6 1.0
O A:HOH1237 5.0 34.4 1.0

Fluorine binding site 3 out of 6 in 5n9t

Go back to Fluorine Binding Sites List in 5n9t
Fluorine binding site 3 out of 6 in the Crystal Structure of USP7 in Complex with A Potent, Selective and Reversible Small-Molecule Inhibitor


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of Crystal Structure of USP7 in Complex with A Potent, Selective and Reversible Small-Molecule Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F1005

b:31.1
occ:1.00
 F1 A:8QQ1005 0.0 31.1 1.0
C17 A:8QQ1005 1.3 26.5 1.0
F A:8QQ1005 2.1 30.8 1.0
F2 A:8QQ1005 2.2 30.1 1.0
C15 A:8QQ1005 2.3 26.7 1.0
C14 A:8QQ1005 2.7 28.3 1.0
C A:ASN460 2.9 29.0 1.0
N A:HIS461 3.0 30.7 1.0
CA A:ASN460 3.0 31.9 1.0
ND1 A:HIS461 3.4 32.1 1.0
O A:ASN460 3.4 32.5 1.0
CE1 A:HIS461 3.7 36.5 1.0
C16 A:8QQ1005 3.7 27.7 1.0
CG A:HIS461 3.7 34.4 1.0
N A:ASN460 3.7 31.8 1.0
CA A:HIS461 3.7 30.6 1.0
O A:HOH1237 3.8 34.4 1.0
O A:HOH1315 3.9 47.3 1.0
C13 A:8QQ1005 4.1 29.2 1.0
NE2 A:HIS461 4.2 32.4 1.0
CD2 A:HIS461 4.2 33.3 1.0
CB A:HIS461 4.3 33.6 1.0
O A:ASP459 4.3 31.2 1.0
C A:ASP459 4.3 34.2 1.0
CB A:ASN460 4.3 36.7 1.0
O1 A:8QQ1005 4.4 30.0 1.0
OH A:TYR465 4.4 27.1 1.0
C24 A:8QQ1005 4.4 27.4 1.0
NE2 A:HIS456 4.4 28.6 1.0
CE1 A:HIS456 4.6 27.5 1.0
C28 A:8QQ1005 4.7 29.4 1.0
CZ A:PHE409 4.8 37.4 1.0
CE1 A:PHE409 4.9 35.8 1.0

Fluorine binding site 4 out of 6 in 5n9t

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Fluorine binding site 4 out of 6 in the Crystal Structure of USP7 in Complex with A Potent, Selective and Reversible Small-Molecule Inhibitor


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 4 of Crystal Structure of USP7 in Complex with A Potent, Selective and Reversible Small-Molecule Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F1003

b:31.8
occ:1.00
 F2 B:8QQ1003 0.0 31.8 1.0
C17 B:8QQ1003 1.3 28.2 1.0
F B:8QQ1003 2.2 34.4 1.0
F1 B:8QQ1003 2.2 31.8 1.0
C15 B:8QQ1003 2.3 28.1 1.0
C16 B:8QQ1003 2.8 27.6 1.0
C B:ASP459 3.1 28.6 1.0
N B:ASN460 3.2 31.4 1.0
CE1 B:HIS456 3.2 33.6 1.0
O B:ASP459 3.3 33.1 1.0
CA B:ASN460 3.4 31.3 1.0
C24 B:8QQ1003 3.4 27.1 1.0
C14 B:8QQ1003 3.6 26.6 1.0
C B:ASN460 3.6 30.4 1.0
C28 B:8QQ1003 3.7 28.9 1.0
CA B:ASP459 3.7 34.0 1.0
O B:ASN460 3.7 29.0 1.0
NE2 B:HIS456 3.8 31.1 1.0
CD B:LYS420 3.8 33.1 1.0
ND1 B:HIS456 3.9 28.5 1.0
CB B:LYS420 4.2 33.8 1.0
O B:GLY458 4.3 36.8 1.0
N B:HIS461 4.4 28.9 1.0
CG B:LYS420 4.4 31.6 1.0
N B:ASP459 4.4 32.1 1.0
C25 B:8QQ1003 4.5 30.8 1.0
O B:HOH1314 4.7 51.0 1.0
C B:GLY458 4.7 36.3 1.0
C27 B:8QQ1003 4.7 29.7 1.0
O B:HOH1250 4.8 41.2 1.0
CE B:LYS420 4.8 30.3 1.0
CD2 B:HIS456 4.8 29.8 1.0
C13 B:8QQ1003 4.8 27.6 1.0
CG B:HIS456 4.8 28.1 1.0
CB B:ASN460 4.9 32.7 1.0
CE1 B:PHE409 4.9 41.5 1.0
CB B:ASP459 4.9 36.7 1.0

Fluorine binding site 5 out of 6 in 5n9t

Go back to Fluorine Binding Sites List in 5n9t
Fluorine binding site 5 out of 6 in the Crystal Structure of USP7 in Complex with A Potent, Selective and Reversible Small-Molecule Inhibitor


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 5 of Crystal Structure of USP7 in Complex with A Potent, Selective and Reversible Small-Molecule Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F1003

b:34.4
occ:1.00
 F B:8QQ1003 0.0 34.4 1.0
C17 B:8QQ1003 1.3 28.2 1.0
F1 B:8QQ1003 2.2 31.8 1.0
F2 B:8QQ1003 2.2 31.8 1.0
C15 B:8QQ1003 2.4 28.1 1.0
C14 B:8QQ1003 2.9 26.6 1.0
CE1 B:PHE409 2.9 41.5 1.0
C24 B:8QQ1003 3.0 27.1 1.0
C16 B:8QQ1003 3.1 27.6 1.0
CZ B:PHE409 3.2 38.3 1.0
CD1 B:PHE409 3.4 34.4 1.0
O B:ASP459 3.8 33.1 1.0
O B:HOH1314 3.9 51.0 1.0
CE2 B:PHE409 4.0 37.7 1.0
CG B:PHE409 4.1 33.8 1.0
CB B:LYS420 4.3 33.8 1.0
C25 B:8QQ1003 4.3 30.8 1.0
C13 B:8QQ1003 4.3 27.6 1.0
O B:HOH1250 4.3 41.2 1.0
CD2 B:PHE409 4.3 35.3 1.0
C B:ASP459 4.4 28.6 1.0
C28 B:8QQ1003 4.4 28.9 1.0
CA B:ASN460 4.4 31.3 1.0
CE1 B:HIS461 4.7 33.5 1.0
N B:ASN460 4.7 31.4 1.0
C B:ASN460 4.8 30.4 1.0
ND1 B:HIS461 4.8 29.7 1.0
N B:LYS420 4.9 32.3 1.0
CG B:LYS420 4.9 31.6 1.0
CD B:LYS420 5.0 33.1 1.0

Fluorine binding site 6 out of 6 in 5n9t

Go back to Fluorine Binding Sites List in 5n9t
Fluorine binding site 6 out of 6 in the Crystal Structure of USP7 in Complex with A Potent, Selective and Reversible Small-Molecule Inhibitor


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 6 of Crystal Structure of USP7 in Complex with A Potent, Selective and Reversible Small-Molecule Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F1003

b:31.8
occ:1.00
 F1 B:8QQ1003 0.0 31.8 1.0
C17 B:8QQ1003 1.4 28.2 1.0
F B:8QQ1003 2.2 34.4 1.0
F2 B:8QQ1003 2.2 31.8 1.0
C15 B:8QQ1003 2.3 28.1 1.0
C14 B:8QQ1003 2.8 26.6 1.0
C B:ASN460 2.9 30.4 1.0
N B:HIS461 3.0 28.9 1.0
CA B:ASN460 3.1 31.3 1.0
ND1 B:HIS461 3.4 29.7 1.0
O B:ASN460 3.5 29.0 1.0
CA B:HIS461 3.6 32.0 1.0
CG B:HIS461 3.7 30.6 1.0
O B:HOH1209 3.7 33.4 1.0
CE1 B:HIS461 3.7 33.5 1.0
C16 B:8QQ1003 3.7 27.6 1.0
N B:ASN460 3.8 31.4 1.0
O B:HOH1314 3.9 51.0 1.0
O B:ASP459 3.9 33.1 1.0
C B:ASP459 4.1 28.6 1.0
CD2 B:HIS461 4.1 27.4 1.0
NE2 B:HIS461 4.1 30.5 1.0
C13 B:8QQ1003 4.1 27.6 1.0
CB B:HIS461 4.2 30.8 1.0
OH B:TYR465 4.3 29.1 1.0
CB B:ASN460 4.3 32.7 1.0
O1 B:8QQ1003 4.4 29.1 1.0
C24 B:8QQ1003 4.4 27.1 1.0
CE1 B:HIS456 4.6 33.6 1.0
NE2 B:HIS456 4.6 31.1 1.0
CZ B:PHE409 4.7 38.3 1.0
C28 B:8QQ1003 4.7 28.9 1.0
CE1 B:PHE409 4.8 41.5 1.0
C B:HIS461 5.0 28.8 1.0

Reference:

G.Gavory, C.R.O'dowd, M.D.Helm, J.Flasz, E.Arkoudis, A.Dossang, C.Hughes, E.Cassidy, K.Mcclelland, E.Odrzywol, N.Page, O.Barker, H.Miel, T.Harrison. Discovery and Characterization of Highly Potent and Selective Allosteric USP7 Inhibitors. Nat. Chem. Biol. V. 14 118 2018.
ISSN: ESSN 1552-4469
PubMed: 29200206
DOI: 10.1038/NCHEMBIO.2528
Page generated: Tue Jul 15 05:26:44 2025

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