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Fluorine in PDB 5a2s: Potent, Selective and Cns-Penetrant Tetrasubstituted Cyclopropane Class Iia Histone Deacetylase (Hdac) Inhibitors

Enzymatic activity of Potent, Selective and Cns-Penetrant Tetrasubstituted Cyclopropane Class Iia Histone Deacetylase (Hdac) Inhibitors

All present enzymatic activity of Potent, Selective and Cns-Penetrant Tetrasubstituted Cyclopropane Class Iia Histone Deacetylase (Hdac) Inhibitors:
3.5.1.98;

Protein crystallography data

The structure of Potent, Selective and Cns-Penetrant Tetrasubstituted Cyclopropane Class Iia Histone Deacetylase (Hdac) Inhibitors, PDB code: 5a2s was solved by C.A.Luckhurst, P.Breccia, A.J.Stott, O.Aziz, H.Birch, R.W.Burli, S.Hughes, R.E.Jarvis, M.Lamers, P.Leonard, K.L.Matthews, G.Mcallister, S.Pollack, E.Saville-Stones, G.Wishart, D.Yates, C.Dominguez, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 161.63 / 2.65
Space group P 2 21 21
Cell size a, b, c (Å), α, β, γ (°) 52.948, 82.141, 161.626, 90.00, 90.00, 90.00
R / Rfree (%) 18.523 / 25.647

Other elements in 5a2s:

The structure of Potent, Selective and Cns-Penetrant Tetrasubstituted Cyclopropane Class Iia Histone Deacetylase (Hdac) Inhibitors also contains other interesting chemical elements:

Zinc (Zn) 4 atoms
Sodium (Na) 2 atoms

Fluorine Binding Sites:

The binding sites of Fluorine atom in the Potent, Selective and Cns-Penetrant Tetrasubstituted Cyclopropane Class Iia Histone Deacetylase (Hdac) Inhibitors (pdb code 5a2s). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 4 binding sites of Fluorine where determined in the Potent, Selective and Cns-Penetrant Tetrasubstituted Cyclopropane Class Iia Histone Deacetylase (Hdac) Inhibitors, PDB code: 5a2s:
Jump to Fluorine binding site number: 1; 2; 3; 4;

Fluorine binding site 1 out of 4 in 5a2s

Go back to Fluorine Binding Sites List in 5a2s
Fluorine binding site 1 out of 4 in the Potent, Selective and Cns-Penetrant Tetrasubstituted Cyclopropane Class Iia Histone Deacetylase (Hdac) Inhibitors


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of Potent, Selective and Cns-Penetrant Tetrasubstituted Cyclopropane Class Iia Histone Deacetylase (Hdac) Inhibitors within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F1

b:22.8
occ:1.00
F5 A:OTF1 0.0 22.8 1.0
C2 A:OTF1 1.3 22.8 1.0
C4 A:OTF1 2.3 22.7 1.0
C1 A:OTF1 2.4 22.5 1.0
C3 A:OTF1 2.4 23.5 1.0
N7 A:OTF1 2.6 22.6 1.0
C15 A:OTF1 2.7 25.1 1.0
C16 A:OTF1 3.1 26.3 1.0
NE2 A:HIS803 3.5 21.4 1.0
O6 A:OTF1 3.5 21.7 1.0
C20 A:OTF1 3.5 26.2 1.0
CD2 A:HIS803 3.6 21.4 1.0
C9 A:OTF1 3.6 22.4 1.0
O A:GLY811 3.7 25.2 1.0
CE1 A:PHE871 3.7 20.3 1.0
O8 A:OTF1 3.9 22.1 1.0
CA A:GLY811 4.0 25.6 1.0
C17 A:OTF1 4.1 26.8 1.0
C A:GLY811 4.1 25.0 1.0
C14 A:OTF1 4.2 22.2 1.0
CD1 A:PHE871 4.2 20.4 1.0
C19 A:OTF1 4.5 26.8 1.0
CZ A:PHE871 4.6 20.2 1.0
ND1 A:HIS842 4.6 19.1 1.0
CE1 A:HIS803 4.7 21.6 1.0
C18 A:OTF1 4.7 27.3 1.0
CE1 A:HIS842 4.7 19.4 1.0
CD2 A:PHE812 4.7 24.9 1.0
C10 A:OTF1 4.7 22.4 1.0
ZN A:ZN2 4.8 20.1 1.0
CG A:HIS803 4.9 21.3 1.0
CG A:HIS842 5.0 18.9 1.0

Fluorine binding site 2 out of 4 in 5a2s

Go back to Fluorine Binding Sites List in 5a2s
Fluorine binding site 2 out of 4 in the Potent, Selective and Cns-Penetrant Tetrasubstituted Cyclopropane Class Iia Histone Deacetylase (Hdac) Inhibitors


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of Potent, Selective and Cns-Penetrant Tetrasubstituted Cyclopropane Class Iia Histone Deacetylase (Hdac) Inhibitors within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F1

b:32.6
occ:1.00
F27 A:OTF1 0.0 32.6 1.0
C24 A:OTF1 1.3 30.5 1.0
C25 A:OTF1 2.4 30.1 1.0
C23 A:OTF1 2.4 29.7 1.0
N26 A:OTF1 3.6 29.7 1.0
N22 A:OTF1 3.6 29.2 1.0
C21 A:OTF1 4.1 28.4 1.0
CD2 A:PHE871 4.9 20.6 1.0

Fluorine binding site 3 out of 4 in 5a2s

Go back to Fluorine Binding Sites List in 5a2s
Fluorine binding site 3 out of 4 in the Potent, Selective and Cns-Penetrant Tetrasubstituted Cyclopropane Class Iia Histone Deacetylase (Hdac) Inhibitors


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of Potent, Selective and Cns-Penetrant Tetrasubstituted Cyclopropane Class Iia Histone Deacetylase (Hdac) Inhibitors within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F1

b:28.5
occ:1.00
F5 B:OTF1 0.0 28.5 1.0
C2 B:OTF1 1.3 27.9 1.0
C1 B:OTF1 2.4 26.2 1.0
C4 B:OTF1 2.4 28.2 1.0
C3 B:OTF1 2.4 28.4 1.0
N7 B:OTF1 2.6 25.0 1.0
C15 B:OTF1 2.8 29.0 1.0
C16 B:OTF1 3.0 29.1 1.0
CE2 B:PHE871 3.2 22.0 1.0
O6 B:OTF1 3.5 25.7 1.0
NE2 B:HIS803 3.6 23.3 1.0
CD2 B:PHE871 3.7 22.0 1.0
C9 B:OTF1 3.7 28.7 1.0
CD2 B:HIS803 3.8 23.7 1.0
C20 B:OTF1 3.8 30.0 1.0
O B:GLY811 3.8 22.5 1.0
CA B:GLY811 3.9 23.4 1.0
O8 B:OTF1 4.0 23.9 1.0
C17 B:OTF1 4.1 29.2 1.0
ND1 B:HIS842 4.2 20.4 1.0
C B:GLY811 4.2 22.7 1.0
CZ B:PHE871 4.2 21.7 1.0
C14 B:OTF1 4.3 29.2 1.0
CE1 B:HIS842 4.4 20.6 1.0
CE1 B:HIS803 4.6 23.5 1.0
CG B:HIS842 4.6 20.6 1.0
C19 B:OTF1 4.7 30.8 1.0
ZN B:ZN2 4.7 22.4 1.0
C10 B:OTF1 4.8 29.1 1.0
CG B:HIS803 4.8 23.4 1.0
C18 B:OTF1 4.9 30.4 1.0
CG B:PHE871 4.9 21.8 1.0
NE2 B:HIS842 5.0 20.8 1.0

Fluorine binding site 4 out of 4 in 5a2s

Go back to Fluorine Binding Sites List in 5a2s
Fluorine binding site 4 out of 4 in the Potent, Selective and Cns-Penetrant Tetrasubstituted Cyclopropane Class Iia Histone Deacetylase (Hdac) Inhibitors


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 4 of Potent, Selective and Cns-Penetrant Tetrasubstituted Cyclopropane Class Iia Histone Deacetylase (Hdac) Inhibitors within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F1

b:32.6
occ:1.00
F27 B:OTF1 0.0 32.6 1.0
C24 B:OTF1 1.4 33.3 1.0
C23 B:OTF1 2.4 32.5 1.0
C25 B:OTF1 2.4 32.4 1.0
N22 B:OTF1 3.6 32.0 1.0
N26 B:OTF1 3.7 31.3 1.0
C21 B:OTF1 4.1 31.3 1.0

Reference:

C.A.Luckhurst, P.Breccia, A.J.Stott, O.Aziz, H.L.Birch, R.W.Burli, S.J.Hughes, R.E.Jarvis, M.Lamers, P.M.Leonard, K.L.Matthews, G.Mcallister, S.Pollack, E.Saville-Stones, G.Wishart, D.Yates, C.Dominguez. Potent, Selective, and Cns-Penetrant Tetrasubstituted Cyclopropane Class Iia Histone Deacetylase (Hdac) Inhibitors. Acs Med.Chem.Lett. V. 7 34 2016.
ISSN: ISSN 1948-5875
PubMed: 26819662
DOI: 10.1021/ACSMEDCHEMLETT.5B00302
Page generated: Tue Jul 15 02:08:43 2025

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