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Fluorine in PDB 6uil: Crystal Structure of Danio Rerio Histone Deacetylase 10 in Complex with 7-[(3-Aminopropyl)Amino]-1,1,1-Trifluoroheptan-2-One

Enzymatic activity of Crystal Structure of Danio Rerio Histone Deacetylase 10 in Complex with 7-[(3-Aminopropyl)Amino]-1,1,1-Trifluoroheptan-2-One

All present enzymatic activity of Crystal Structure of Danio Rerio Histone Deacetylase 10 in Complex with 7-[(3-Aminopropyl)Amino]-1,1,1-Trifluoroheptan-2-One:
3.5.1.48; 3.5.1.62;

Protein crystallography data

The structure of Crystal Structure of Danio Rerio Histone Deacetylase 10 in Complex with 7-[(3-Aminopropyl)Amino]-1,1,1-Trifluoroheptan-2-One, PDB code: 6uil was solved by C.J.Herbst-Gervasoni, D.W.Christianson, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 45.90 / 2.85
Space group P 31 2 1
Cell size a, b, c (Å), α, β, γ (°) 80.980, 80.980, 242.822, 90.00, 90.00, 120.00
R / Rfree (%) 24.4 / 30.6

Other elements in 6uil:

The structure of Crystal Structure of Danio Rerio Histone Deacetylase 10 in Complex with 7-[(3-Aminopropyl)Amino]-1,1,1-Trifluoroheptan-2-One also contains other interesting chemical elements:

Potassium (K) 2 atoms
Zinc (Zn) 1 atom

Fluorine Binding Sites:

The binding sites of Fluorine atom in the Crystal Structure of Danio Rerio Histone Deacetylase 10 in Complex with 7-[(3-Aminopropyl)Amino]-1,1,1-Trifluoroheptan-2-One (pdb code 6uil). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 3 binding sites of Fluorine where determined in the Crystal Structure of Danio Rerio Histone Deacetylase 10 in Complex with 7-[(3-Aminopropyl)Amino]-1,1,1-Trifluoroheptan-2-One, PDB code: 6uil:
Jump to Fluorine binding site number: 1; 2; 3;

Fluorine binding site 1 out of 3 in 6uil

Go back to Fluorine Binding Sites List in 6uil
Fluorine binding site 1 out of 3 in the Crystal Structure of Danio Rerio Histone Deacetylase 10 in Complex with 7-[(3-Aminopropyl)Amino]-1,1,1-Trifluoroheptan-2-One


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 Danio Rerio Histone Deacetylase 10 in Complex with 7-[(3-Aminopropyl)Amino]-1,1,1-Trifluoroheptan-2-One within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F701

b:52.1
occ:1.00
 F15 A:FKS701 0.0 52.1 1.0
C12 A:FKS701 1.3 59.1 1.0
F17 A:FKS701 2.1 64.3 1.0
F16 A:FKS701 2.1 43.0 1.0
C11 A:FKS701 2.4 58.9 1.0
OD2 A:ASP174 2.6 56.6 1.0
O14 A:FKS701 2.7 51.8 1.0
O13 A:FKS701 2.9 62.3 1.0
N A:GLY305 2.9 68.5 1.0
C A:GLU304 3.1 63.7 1.0
CA A:GLY305 3.2 59.2 1.0
CB A:GLU304 3.3 58.1 1.0
NE2 A:HIS136 3.4 51.4 1.0
ZN A:ZN704 3.4 60.0 1.0
O A:GLU304 3.6 71.5 1.0
CA A:GLU304 3.7 51.3 1.0
C10 A:FKS701 3.8 60.5 1.0
CG A:ASP174 3.8 56.4 1.0
OE1 A:GLU304 4.0 54.5 1.0
CE1 A:HIS136 4.0 51.7 1.0
CB A:PRO134 4.1 59.2 1.0
CD2 A:HIS136 4.1 58.2 1.0
OH A:TYR307 4.3 64.4 1.0
CG A:GLU304 4.5 60.6 1.0
CG A:PRO134 4.5 50.6 1.0
OD1 A:ASP174 4.6 64.9 1.0
CD A:GLU304 4.7 61.2 1.0
CB A:ASP174 4.7 56.2 1.0
C A:GLY305 4.7 66.1 1.0
OD2 A:ASP267 4.9 55.3 1.0

Fluorine binding site 2 out of 3 in 6uil

Go back to Fluorine Binding Sites List in 6uil
Fluorine binding site 2 out of 3 in the Crystal Structure of Danio Rerio Histone Deacetylase 10 in Complex with 7-[(3-Aminopropyl)Amino]-1,1,1-Trifluoroheptan-2-One


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 Danio Rerio Histone Deacetylase 10 in Complex with 7-[(3-Aminopropyl)Amino]-1,1,1-Trifluoroheptan-2-One within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F701

b:43.0
occ:1.00
 F16 A:FKS701 0.0 43.0 1.0
C12 A:FKS701 1.3 59.1 1.0
F15 A:FKS701 2.1 52.1 1.0
F17 A:FKS701 2.1 64.3 1.0
C11 A:FKS701 2.5 58.9 1.0
O14 A:FKS701 2.9 51.8 1.0
C10 A:FKS701 3.0 60.5 1.0
CB A:PRO134 3.2 59.2 1.0
NE2 A:HIS136 3.4 51.4 1.0
SG A:CYS147 3.4 57.0 1.0
O13 A:FKS701 3.6 62.3 1.0
CD2 A:HIS136 3.6 58.2 1.0
CG A:PRO134 3.7 50.6 1.0
NE2 A:HIS137 4.0 56.2 1.0
OE1 A:GLU304 4.0 54.5 1.0
CD2 A:HIS137 4.2 62.5 1.0
OD2 A:ASP174 4.2 56.6 1.0
CE1 A:HIS137 4.4 60.7 1.0
C9 A:FKS701 4.5 52.5 1.0
C A:GLU304 4.5 63.7 1.0
CE1 A:HIS136 4.5 51.7 1.0
O A:GLU304 4.5 71.5 1.0
CG A:HIS137 4.6 60.2 1.0
OH A:TYR307 4.6 64.4 1.0
CA A:PRO134 4.6 59.6 1.0
CB A:GLU304 4.7 58.1 1.0
ZN A:ZN704 4.7 60.0 1.0
ND1 A:HIS137 4.7 61.9 1.0
N A:GLY135 4.7 65.0 1.0
N A:GLY305 4.7 68.5 1.0
CG A:HIS136 4.9 56.2 1.0
CB A:PHE146 4.9 60.7 1.0
CD A:PRO134 4.9 64.0 1.0
N A:PHE146 4.9 70.0 1.0
CA A:GLU304 4.9 51.3 1.0
CA A:GLY305 5.0 59.2 1.0

Fluorine binding site 3 out of 3 in 6uil

Go back to Fluorine Binding Sites List in 6uil
Fluorine binding site 3 out of 3 in the Crystal Structure of Danio Rerio Histone Deacetylase 10 in Complex with 7-[(3-Aminopropyl)Amino]-1,1,1-Trifluoroheptan-2-One


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 Danio Rerio Histone Deacetylase 10 in Complex with 7-[(3-Aminopropyl)Amino]-1,1,1-Trifluoroheptan-2-One within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F701

b:64.3
occ:1.00
 F17 A:FKS701 0.0 64.3 1.0
C12 A:FKS701 1.3 59.1 1.0
F15 A:FKS701 2.1 52.1 1.0
F16 A:FKS701 2.1 43.0 1.0
C11 A:FKS701 2.5 58.9 1.0
O13 A:FKS701 2.8 62.3 1.0
OH A:TYR307 3.0 64.4 1.0
CG A:PRO134 3.1 50.6 1.0
C10 A:FKS701 3.2 60.5 1.0
O A:GLU304 3.2 71.5 1.0
CA A:GLY305 3.4 59.2 1.0
CB A:PRO134 3.4 59.2 1.0
C A:GLU304 3.5 63.7 1.0
O14 A:FKS701 3.6 51.8 1.0
N A:GLY305 3.6 68.5 1.0
CZ A:TYR307 4.1 67.3 1.0
CD2 A:PHE146 4.2 59.3 1.0
ZN A:ZN704 4.4 60.0 1.0
C9 A:FKS701 4.4 52.5 1.0
CD A:PRO134 4.5 64.0 1.0
CA A:GLU304 4.5 51.3 1.0
OD2 A:ASP174 4.5 56.6 1.0
CB A:PHE146 4.6 60.7 1.0
CB A:GLU304 4.7 58.1 1.0
CE1 A:TYR307 4.8 69.8 1.0
C A:GLY305 4.8 66.1 1.0
CE2 A:TYR307 4.9 61.9 1.0
CA A:PRO134 4.9 59.6 1.0
CG A:PHE146 4.9 62.7 1.0

Reference:

C.J.Herbst-Gervasoni, D.W.Christianson. Binding of N8-Acetylspermidine Analogues to Histone Deacetylase 10 Reveals Molecular Strategies For Blocking Polyamine Deacetylation. Biochemistry 2019.
ISSN: ISSN 0006-2960
PubMed: 31746596
DOI: 10.1021/ACS.BIOCHEM.9B00906
Page generated: Tue Jul 15 16:18:30 2025

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