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Fluorine in PDB 5nge: Crystal Structure of USP7 in Complex with the Non-Covalent Inhibitor, FT671

Enzymatic activity of Crystal Structure of USP7 in Complex with the Non-Covalent Inhibitor, FT671

All present enzymatic activity of Crystal Structure of USP7 in Complex with the Non-Covalent Inhibitor, FT671:
3.4.19.12;

Protein crystallography data

The structure of Crystal Structure of USP7 in Complex with the Non-Covalent Inhibitor, FT671, PDB code: 5nge was solved by A.P.Turnbull, W.W.Krajewski, S.Ioannidis, B.M.Kessler, D.Komander, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 50.00 / 2.35
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 71.280, 70.300, 78.560, 90.00, 97.17, 90.00
R / Rfree (%) 21.4 / 27.2

Fluorine Binding Sites:

The binding sites of Fluorine atom in the Crystal Structure of USP7 in Complex with the Non-Covalent Inhibitor, FT671 (pdb code 5nge). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 8 binding sites of Fluorine where determined in the Crystal Structure of USP7 in Complex with the Non-Covalent Inhibitor, FT671, PDB code: 5nge:
Jump to Fluorine binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Fluorine binding site 1 out of 8 in 5nge

Go back to Fluorine Binding Sites List in 5nge
Fluorine binding site 1 out of 8 in the Crystal Structure of USP7 in Complex with the Non-Covalent Inhibitor, FT671


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 the Non-Covalent Inhibitor, FT671 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F601

b:55.8
occ:1.00
 FAD A:8WK601 0.0 55.8 1.0
CAZ A:8WK601 1.4 58.4 1.0
CAH A:8WK601 2.5 58.6 1.0
CAI A:8WK601 2.5 53.3 1.0
CAK A:8WK601 3.7 53.2 1.0
CAJ A:8WK601 3.7 51.9 1.0
OE1 A:GLN351 3.9 49.5 1.0
CBB A:8WK601 4.3 46.1 1.0
CD A:GLN351 4.7 45.8 1.0
CG A:GLN351 4.8 45.9 1.0

Fluorine binding site 2 out of 8 in 5nge

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Fluorine binding site 2 out of 8 in the Crystal Structure of USP7 in Complex with the Non-Covalent Inhibitor, FT671


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 the Non-Covalent Inhibitor, FT671 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F601

b:63.8
occ:1.00
 FAF A:8WK601 0.0 63.8 1.0
CBF A:8WK601 1.4 64.2 1.0
FAG A:8WK601 2.2 66.0 1.0
CBL A:8WK601 2.4 58.5 1.0
NBI A:8WK601 2.9 55.9 1.0
N A:ASN460 3.2 74.2 1.0
CA A:ASN460 3.2 76.1 1.0
O A:ASN460 3.3 79.9 1.0
C A:ASN460 3.3 78.1 1.0
CE1 A:HIS456 3.4 62.7 1.0
CAM A:8WK601 3.4 52.6 1.0
C A:ASP459 3.5 76.2 1.0
O A:ASP459 3.5 77.7 1.0
NE2 A:HIS456 3.6 62.1 1.0
NAX A:8WK601 3.7 51.9 1.0
CAT A:8WK601 3.8 55.7 1.0
N A:HIS461 4.1 78.6 1.0
ND1 A:HIS456 4.1 63.0 1.0
CAL A:8WK601 4.3 52.9 1.0
CE1 A:PHE409 4.4 70.6 1.0
CBA A:8WK601 4.4 53.0 1.0
CD A:LYS420 4.5 67.3 1.0
CA A:ASP459 4.5 77.3 1.0
CD2 A:HIS456 4.5 58.0 1.0
CG A:LYS420 4.5 66.8 1.0
CB A:LYS420 4.6 69.5 1.0
CD1 A:PHE409 4.6 68.8 1.0
CB A:ASN460 4.7 79.6 1.0
CG A:HIS456 4.8 58.2 1.0
CZ A:PHE409 4.8 70.1 1.0
OH A:TYR465 4.8 58.1 1.0
CA A:HIS461 4.9 74.3 1.0
CAY A:8WK601 4.9 57.5 1.0
O A:GLY458 4.9 75.1 1.0
CE A:LYS420 5.0 59.3 1.0

Fluorine binding site 3 out of 8 in 5nge

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Fluorine binding site 3 out of 8 in the Crystal Structure of USP7 in Complex with the Non-Covalent Inhibitor, FT671


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 the Non-Covalent Inhibitor, FT671 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F601

b:66.0
occ:1.00
 FAG A:8WK601 0.0 66.0 1.0
CBF A:8WK601 1.4 64.2 1.0
FAF A:8WK601 2.2 63.8 1.0
CBL A:8WK601 2.5 58.5 1.0
CAT A:8WK601 3.0 55.7 1.0
N A:HIS461 3.0 78.6 1.0
C A:ASN460 3.0 78.1 1.0
ND1 A:HIS461 3.2 70.7 1.0
CA A:ASN460 3.2 76.1 1.0
CE1 A:HIS461 3.5 69.7 1.0
CG A:HIS461 3.5 70.8 1.0
O A:ASN460 3.6 79.9 1.0
CZ A:PHE409 3.6 70.1 1.0
CA A:HIS461 3.7 74.3 1.0
NBI A:8WK601 3.7 55.9 1.0
NE2 A:HIS461 3.9 66.0 1.0
CE1 A:PHE409 3.9 70.6 1.0
CD2 A:HIS461 3.9 67.7 1.0
CB A:HIS461 4.1 73.0 1.0
N A:ASN460 4.1 74.2 1.0
CE2 A:PHE409 4.1 65.2 1.0
O A:ASP459 4.3 77.7 1.0
CB A:ASN460 4.4 79.6 1.0
NAX A:8WK601 4.4 51.9 1.0
CAY A:8WK601 4.4 57.5 1.0
OH A:TYR465 4.5 58.1 1.0
CD1 A:PHE409 4.6 68.8 1.0
C A:ASP459 4.6 76.2 1.0
CAM A:8WK601 4.7 52.6 1.0
CD2 A:PHE409 4.8 62.1 1.0
OAA A:8WK601 4.9 63.5 1.0
CG A:PHE409 5.0 63.2 1.0

Fluorine binding site 4 out of 8 in 5nge

Go back to Fluorine Binding Sites List in 5nge
Fluorine binding site 4 out of 8 in the Crystal Structure of USP7 in Complex with the Non-Covalent Inhibitor, FT671


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 the Non-Covalent Inhibitor, FT671 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F601

b:59.4
occ:1.00
 FAE A:8WK601 0.0 59.4 1.0
CBA A:8WK601 1.2 53.0 1.0
CAL A:8WK601 2.2 52.9 1.0
NAX A:8WK601 2.2 51.9 1.0
CAM A:8WK601 3.3 52.6 1.0
NBI A:8WK601 3.3 55.9 1.0
CB A:ARG408 3.3 59.0 1.0
OAB A:8WK601 3.7 46.6 1.0
N A:PHE409 3.7 65.4 1.0
CB A:PHE409 3.7 62.7 1.0
CAS A:8WK601 3.8 44.6 1.0
C A:ARG408 3.9 66.2 1.0
CB A:TYR514 3.9 43.9 1.0
CA A:ARG408 4.0 61.0 1.0
CA A:PHE409 4.2 67.9 1.0
CAU A:8WK601 4.3 41.2 1.0
CAR A:8WK601 4.3 49.2 1.0
CBK A:8WK601 4.4 46.5 1.0
N A:ARG408 4.4 59.9 1.0
CG A:LYS420 4.4 66.8 1.0
CG A:ARG408 4.4 57.6 1.0
CE A:LYS420 4.5 59.3 1.0
O A:ARG408 4.5 72.4 1.0
CAQ A:8WK601 4.5 46.8 1.0
CG A:PHE409 4.6 63.2 1.0
CBL A:8WK601 4.6 58.5 1.0
CG A:TYR514 4.6 45.7 1.0
CD A:ARG408 4.7 56.5 1.0
NBG A:8WK601 4.7 47.9 1.0
CBC A:8WK601 4.7 54.5 1.0
O A:LEU406 4.9 50.7 1.0
CD1 A:PHE409 4.9 68.8 1.0
CAY A:8WK601 5.0 57.5 1.0
NBH A:8WK601 5.0 46.5 1.0

Fluorine binding site 5 out of 8 in 5nge

Go back to Fluorine Binding Sites List in 5nge
Fluorine binding site 5 out of 8 in the Crystal Structure of USP7 in Complex with the Non-Covalent Inhibitor, FT671


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 the Non-Covalent Inhibitor, FT671 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F601

b:56.7
occ:1.00
 FAD B:8WK601 0.0 56.7 1.0
CAZ B:8WK601 1.5 56.6 1.0
CAH B:8WK601 2.5 55.6 1.0
CAI B:8WK601 2.6 54.5 1.0
CAJ B:8WK601 3.8 58.6 1.0
CAK B:8WK601 3.9 51.3 1.0
OE1 B:GLN351 3.9 54.6 1.0
CBB B:8WK601 4.3 52.7 1.0
CD B:GLN351 4.7 54.2 1.0
CG B:GLN351 4.9 56.4 1.0

Fluorine binding site 6 out of 8 in 5nge

Go back to Fluorine Binding Sites List in 5nge
Fluorine binding site 6 out of 8 in the Crystal Structure of USP7 in Complex with the Non-Covalent Inhibitor, FT671


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 the Non-Covalent Inhibitor, FT671 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F601

b:55.6
occ:1.00
 FAF B:8WK601 0.0 55.6 1.0
CBF B:8WK601 1.4 63.5 1.0
FAG B:8WK601 2.4 69.5 1.0
CBL B:8WK601 2.4 56.5 1.0
NBI B:8WK601 3.0 52.2 1.0
CA B:ASN460 3.2 78.3 1.0
N B:ASN460 3.2 80.8 1.0
C B:ASN460 3.3 77.0 1.0
O B:ASN460 3.3 70.8 1.0
O B:ASP459 3.4 93.8 1.0
C B:ASP459 3.4 88.7 1.0
CE1 B:HIS456 3.5 63.2 1.0
CAM B:8WK601 3.7 55.5 1.0
NAX B:8WK601 3.7 53.0 1.0
CAT B:8WK601 3.8 52.9 1.0
NE2 B:HIS456 3.8 62.4 1.0
N B:HIS461 4.0 77.3 1.0
ND1 B:HIS456 4.2 61.3 1.0
CE1 B:PHE409 4.3 74.5 1.0
CD B:LYS420 4.4 70.9 1.0
CG B:LYS420 4.4 71.9 1.0
CB B:LYS420 4.4 74.1 1.0
CA B:ASP459 4.4 90.2 1.0
CD1 B:PHE409 4.6 74.9 1.0
CBA B:8WK601 4.6 58.7 1.0
CAL B:8WK601 4.6 52.3 1.0
CB B:ASN460 4.7 81.7 1.0
CD2 B:HIS456 4.7 59.4 1.0
CZ B:PHE409 4.8 71.5 1.0
O B:GLY458 4.8 78.0 1.0
CE B:LYS420 4.9 63.7 1.0
CA B:HIS461 4.9 73.8 1.0
CG B:HIS456 4.9 58.4 1.0
CAY B:8WK601 4.9 53.7 1.0
N B:ASP459 4.9 87.6 1.0
OH B:TYR465 5.0 56.2 1.0

Fluorine binding site 7 out of 8 in 5nge

Go back to Fluorine Binding Sites List in 5nge
Fluorine binding site 7 out of 8 in the Crystal Structure of USP7 in Complex with the Non-Covalent Inhibitor, FT671


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 7 of Crystal Structure of USP7 in Complex with the Non-Covalent Inhibitor, FT671 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F601

b:69.5
occ:1.00
 FAG B:8WK601 0.0 69.5 1.0
CBF B:8WK601 1.5 63.5 1.0
FAF B:8WK601 2.4 55.6 1.0
CBL B:8WK601 2.5 56.5 1.0
CAT B:8WK601 2.8 52.9 1.0
CZ B:PHE409 3.2 71.5 1.0
ND1 B:HIS461 3.2 74.5 1.0
CE1 B:HIS461 3.3 71.5 1.0
N B:HIS461 3.4 77.3 1.0
CE1 B:PHE409 3.4 74.5 1.0
C B:ASN460 3.5 77.0 1.0
CA B:ASN460 3.6 78.3 1.0
CE2 B:PHE409 3.7 69.3 1.0
CG B:HIS461 3.7 73.8 1.0
NBI B:8WK601 3.7 52.2 1.0
NE2 B:HIS461 3.9 70.3 1.0
CD2 B:HIS461 4.1 70.1 1.0
CD1 B:PHE409 4.1 74.9 1.0
O B:ASN460 4.1 70.8 1.0
CA B:HIS461 4.1 73.8 1.0
NAX B:8WK601 4.2 53.0 1.0
CD2 B:PHE409 4.3 69.7 1.0
CAY B:8WK601 4.3 53.7 1.0
O B:ASP459 4.4 93.8 1.0
CB B:HIS461 4.4 73.0 1.0
N B:ASN460 4.4 80.8 1.0
CG B:PHE409 4.5 70.1 1.0
CB B:ASN460 4.7 81.7 1.0
C B:ASP459 4.8 88.7 1.0
OAA B:8WK601 4.8 57.2 1.0
OH B:TYR465 4.9 56.2 1.0
CAM B:8WK601 4.9 55.5 1.0

Fluorine binding site 8 out of 8 in 5nge

Go back to Fluorine Binding Sites List in 5nge
Fluorine binding site 8 out of 8 in the Crystal Structure of USP7 in Complex with the Non-Covalent Inhibitor, FT671


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 8 of Crystal Structure of USP7 in Complex with the Non-Covalent Inhibitor, FT671 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F601

b:68.2
occ:1.00
 FAE B:8WK601 0.0 68.2 1.0
CBA B:8WK601 1.4 58.7 1.0
NAX B:8WK601 2.4 53.0 1.0
CAL B:8WK601 2.5 52.3 1.0
CB B:ARG408 2.9 65.9 1.0
OAB B:8WK601 3.3 49.6 1.0
N B:PHE409 3.4 67.1 1.0
NBI B:8WK601 3.5 52.2 1.0
C B:ARG408 3.5 70.1 1.0
CAM B:8WK601 3.5 55.5 1.0
CA B:ARG408 3.6 66.3 1.0
CB B:PHE409 3.6 66.1 1.0
N B:ARG408 3.9 61.5 1.0
CAS B:8WK601 3.9 47.9 1.0
CA B:PHE409 4.0 70.5 1.0
CB B:TYR514 4.0 49.4 1.0
CG B:ARG408 4.1 63.6 1.0
O B:ARG408 4.2 76.4 1.0
CAU B:8WK601 4.2 48.2 1.0
CBK B:8WK601 4.4 47.2 1.0
CAR B:8WK601 4.4 45.6 1.0
CBC B:8WK601 4.4 55.9 1.0
CG B:LYS420 4.5 71.9 1.0
O B:LEU406 4.5 50.1 1.0
CD B:ARG408 4.5 61.0 1.0
CG B:PHE409 4.6 70.1 1.0
CE B:LYS420 4.7 63.7 1.0
CBL B:8WK601 4.8 56.5 1.0
CAQ B:8WK601 4.8 50.6 1.0
NBH B:8WK601 4.8 46.8 1.0
NBG B:8WK601 4.9 46.4 1.0
CG B:TYR514 4.9 49.0 1.0
CD1 B:PHE409 5.0 74.9 1.0

Reference:

A.P.Turnbull, S.Ioannidis, W.W.Krajewski, A.Pinto-Fernandez, C.Heride, A.C.L.Martin, L.M.Tonkin, E.C.Townsend, S.M.Buker, D.R.Lancia, J.A.Caravella, A.V.Toms, T.M.Charlton, J.Lahdenranta, E.Wilker, B.C.Follows, N.J.Evans, L.Stead, C.Alli, V.V.Zarayskiy, A.C.Talbot, A.J.Buckmelter, M.Wang, C.L.Mckinnon, F.Saab, J.F.Mcgouran, H.Century, M.Gersch, M.S.Pittman, C.G.Marshall, T.M.Raynham, M.Simcox, L.M.D.Stewart, S.B.Mcloughlin, J.A.Escobedo, K.W.Bair, C.J.Dinsmore, T.R.Hammonds, S.Kim, S.Urbe, M.J.Clague, B.M.Kessler, D.Komander. Molecular Basis of USP7 Inhibition By Selective Small-Molecule Inhibitors. Nature V. 550 481 2017.
ISSN: ESSN 1476-4687
PubMed: 29045389
DOI: 10.1038/NATURE24451
Page generated: Tue Jul 15 05:29:16 2025

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