Atomistry » Fluorine » PDB 5msb-5njh » 5n9t
Atomistry »
  Fluorine »
    PDB 5msb-5njh »
      5n9t »

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

Go back to Fluorine Binding Sites List in 5n9t
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: Thu Aug 1 11:56:21 2024

Last articles

Zn in 9JYW
Zn in 9IR4
Zn in 9IR3
Zn in 9GMX
Zn in 9GMW
Zn in 9JEJ
Zn in 9ERF
Zn in 9ERE
Zn in 9EGV
Zn in 9EGW
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy