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Fluorine in PDB 7ms5: Structure of USP5 Zinc-Finger Ubiquitin Binding Domain Co-Crystallized with 4-(4-(4-(3,4-Difluoro-Phenyl)-Piperidin-1-Ylsulfonyl)-Phenyl)-4- Oxo-Butanoic Acid

Enzymatic activity of Structure of USP5 Zinc-Finger Ubiquitin Binding Domain Co-Crystallized with 4-(4-(4-(3,4-Difluoro-Phenyl)-Piperidin-1-Ylsulfonyl)-Phenyl)-4- Oxo-Butanoic Acid

All present enzymatic activity of Structure of USP5 Zinc-Finger Ubiquitin Binding Domain Co-Crystallized with 4-(4-(4-(3,4-Difluoro-Phenyl)-Piperidin-1-Ylsulfonyl)-Phenyl)-4- Oxo-Butanoic Acid:
3.4.19.12;

Protein crystallography data

The structure of Structure of USP5 Zinc-Finger Ubiquitin Binding Domain Co-Crystallized with 4-(4-(4-(3,4-Difluoro-Phenyl)-Piperidin-1-Ylsulfonyl)-Phenyl)-4- Oxo-Butanoic Acid, PDB code: 7ms5 was solved by M.K.Mann, C.A.Zepeda-Velazquez, H.G.Alvarez, A.Dong, T.Kiyota, A.Aman, C.H.Arrowsmith, R.Al-Awar, R.J.Harding, M.Schapira, Structural Genomicsconsortium (Sgc), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 29.53 / 1.98
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 61.697, 84.494, 59.642, 90, 98.27, 90
R / Rfree (%) 18.2 / 21.6

Other elements in 7ms5:

The structure of Structure of USP5 Zinc-Finger Ubiquitin Binding Domain Co-Crystallized with 4-(4-(4-(3,4-Difluoro-Phenyl)-Piperidin-1-Ylsulfonyl)-Phenyl)-4- Oxo-Butanoic Acid also contains other interesting chemical elements:

Zinc (Zn) 2 atoms
Calcium (Ca) 1 atom

Fluorine Binding Sites:

The binding sites of Fluorine atom in the Structure of USP5 Zinc-Finger Ubiquitin Binding Domain Co-Crystallized with 4-(4-(4-(3,4-Difluoro-Phenyl)-Piperidin-1-Ylsulfonyl)-Phenyl)-4- Oxo-Butanoic Acid (pdb code 7ms5). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 4 binding sites of Fluorine where determined in the Structure of USP5 Zinc-Finger Ubiquitin Binding Domain Co-Crystallized with 4-(4-(4-(3,4-Difluoro-Phenyl)-Piperidin-1-Ylsulfonyl)-Phenyl)-4- Oxo-Butanoic Acid, PDB code: 7ms5:
Jump to Fluorine binding site number: 1; 2; 3; 4;

Fluorine binding site 1 out of 4 in 7ms5

Go back to Fluorine Binding Sites List in 7ms5
Fluorine binding site 1 out of 4 in the Structure of USP5 Zinc-Finger Ubiquitin Binding Domain Co-Crystallized with 4-(4-(4-(3,4-Difluoro-Phenyl)-Piperidin-1-Ylsulfonyl)-Phenyl)-4- Oxo-Butanoic Acid


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of Structure of USP5 Zinc-Finger Ubiquitin Binding Domain Co-Crystallized with 4-(4-(4-(3,4-Difluoro-Phenyl)-Piperidin-1-Ylsulfonyl)-Phenyl)-4- Oxo-Butanoic Acid within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F302

b:25.5
occ:1.00
 F A:ZOG302 0.0 25.5 1.0
C9 A:ZOG302 1.4 22.2 1.0
C8 A:ZOG302 2.3 23.5 1.0
C10 A:ZOG302 2.4 20.4 1.0
F1 A:ZOG302 2.7 30.9 1.0
C7 A:ZOG302 3.6 22.2 1.0
C5 A:ZOG302 3.6 20.5 1.0
C6 A:ZOG302 4.1 20.7 1.0
C4 A:ZOG302 4.9 19.4 1.0

Fluorine binding site 2 out of 4 in 7ms5

Go back to Fluorine Binding Sites List in 7ms5
Fluorine binding site 2 out of 4 in the Structure of USP5 Zinc-Finger Ubiquitin Binding Domain Co-Crystallized with 4-(4-(4-(3,4-Difluoro-Phenyl)-Piperidin-1-Ylsulfonyl)-Phenyl)-4- Oxo-Butanoic Acid


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of Structure of USP5 Zinc-Finger Ubiquitin Binding Domain Co-Crystallized with 4-(4-(4-(3,4-Difluoro-Phenyl)-Piperidin-1-Ylsulfonyl)-Phenyl)-4- Oxo-Butanoic Acid within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F302

b:30.9
occ:1.00
 F1 A:ZOG302 0.0 30.9 1.0
C8 A:ZOG302 1.4 23.5 1.0
C9 A:ZOG302 2.3 22.2 1.0
C7 A:ZOG302 2.4 22.2 1.0
F A:ZOG302 2.7 25.5 1.0
O A:HOH412 3.2 28.2 1.0
C10 A:ZOG302 3.6 20.4 1.0
C6 A:ZOG302 3.6 20.7 1.0
OD2 A:ASP225 3.8 13.2 1.0
C5 A:ZOG302 4.1 20.5 1.0
CG A:ASP225 5.0 14.1 1.0

Fluorine binding site 3 out of 4 in 7ms5

Go back to Fluorine Binding Sites List in 7ms5
Fluorine binding site 3 out of 4 in the Structure of USP5 Zinc-Finger Ubiquitin Binding Domain Co-Crystallized with 4-(4-(4-(3,4-Difluoro-Phenyl)-Piperidin-1-Ylsulfonyl)-Phenyl)-4- Oxo-Butanoic Acid


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of Structure of USP5 Zinc-Finger Ubiquitin Binding Domain Co-Crystallized with 4-(4-(4-(3,4-Difluoro-Phenyl)-Piperidin-1-Ylsulfonyl)-Phenyl)-4- Oxo-Butanoic Acid within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F303

b:37.7
occ:1.00
 F B:ZOG303 0.0 37.7 1.0
C9 B:ZOG303 1.3 33.0 1.0
C10 B:ZOG303 2.3 30.1 1.0
C8 B:ZOG303 2.4 29.9 1.0
F1 B:ZOG303 2.7 31.4 1.0
C7 B:ZOG303 3.6 30.9 1.0
C5 B:ZOG303 3.6 30.5 1.0
C6 B:ZOG303 4.1 29.2 1.0
C4 B:ZOG303 4.8 32.4 1.0

Fluorine binding site 4 out of 4 in 7ms5

Go back to Fluorine Binding Sites List in 7ms5
Fluorine binding site 4 out of 4 in the Structure of USP5 Zinc-Finger Ubiquitin Binding Domain Co-Crystallized with 4-(4-(4-(3,4-Difluoro-Phenyl)-Piperidin-1-Ylsulfonyl)-Phenyl)-4- Oxo-Butanoic Acid


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 4 of Structure of USP5 Zinc-Finger Ubiquitin Binding Domain Co-Crystallized with 4-(4-(4-(3,4-Difluoro-Phenyl)-Piperidin-1-Ylsulfonyl)-Phenyl)-4- Oxo-Butanoic Acid within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F303

b:31.4
occ:1.00
 F1 B:ZOG303 0.0 31.4 1.0
C8 B:ZOG303 1.4 29.9 1.0
C7 B:ZOG303 2.4 30.9 1.0
C9 B:ZOG303 2.4 33.0 1.0
F B:ZOG303 2.7 37.7 1.0
C6 B:ZOG303 3.6 29.2 1.0
C10 B:ZOG303 3.6 30.1 1.0
C5 B:ZOG303 4.1 30.5 1.0

Reference:

M.K.Mann, C.A.Zepeda-Velazquez, H.G.Alvarez, A.Dong, T.Kiyota, A.Aman, C.H.Arrowsmith, R.Al-Awar, R.J.Harding, M.Schapira. Structure Activity Relationship of Allosteric Inhibitors of USP5 To Be Published.
Page generated: Tue Jul 15 21:52:04 2025

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