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Fluorine in PDB 6g3o: Crystal Structure of Human HDAC2 in Complex with (R)-6-[3,4-Dioxo-2- (4-Trifluoromethoxy-Phenylamino)-Cyclobut-1-Enylamino]-Heptanoic Acid Hydroxyamide

Enzymatic activity of Crystal Structure of Human HDAC2 in Complex with (R)-6-[3,4-Dioxo-2- (4-Trifluoromethoxy-Phenylamino)-Cyclobut-1-Enylamino]-Heptanoic Acid Hydroxyamide

All present enzymatic activity of Crystal Structure of Human HDAC2 in Complex with (R)-6-[3,4-Dioxo-2- (4-Trifluoromethoxy-Phenylamino)-Cyclobut-1-Enylamino]-Heptanoic Acid Hydroxyamide:
3.5.1.98;

Protein crystallography data

The structure of Crystal Structure of Human HDAC2 in Complex with (R)-6-[3,4-Dioxo-2- (4-Trifluoromethoxy-Phenylamino)-Cyclobut-1-Enylamino]-Heptanoic Acid Hydroxyamide, PDB code: 6g3o was solved by T.Isabet, M.Aurelly, L.Chantalat, E.Thoreau, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 33.26 / 2.27
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 92.050, 93.300, 139.420, 90.00, 90.00, 90.00
R / Rfree (%) 17.2 / 21.9

Other elements in 6g3o:

The structure of Crystal Structure of Human HDAC2 in Complex with (R)-6-[3,4-Dioxo-2- (4-Trifluoromethoxy-Phenylamino)-Cyclobut-1-Enylamino]-Heptanoic Acid Hydroxyamide also contains other interesting chemical elements:

Zinc (Zn) 3 atoms
Calcium (Ca) 3 atoms
Sodium (Na) 3 atoms

Fluorine Binding Sites:

The binding sites of Fluorine atom in the Crystal Structure of Human HDAC2 in Complex with (R)-6-[3,4-Dioxo-2- (4-Trifluoromethoxy-Phenylamino)-Cyclobut-1-Enylamino]-Heptanoic Acid Hydroxyamide (pdb code 6g3o). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 9 binding sites of Fluorine where determined in the Crystal Structure of Human HDAC2 in Complex with (R)-6-[3,4-Dioxo-2- (4-Trifluoromethoxy-Phenylamino)-Cyclobut-1-Enylamino]-Heptanoic Acid Hydroxyamide, PDB code: 6g3o:
Jump to Fluorine binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9;

Fluorine binding site 1 out of 9 in 6g3o

Go back to Fluorine Binding Sites List in 6g3o
Fluorine binding site 1 out of 9 in the Crystal Structure of Human HDAC2 in Complex with (R)-6-[3,4-Dioxo-2- (4-Trifluoromethoxy-Phenylamino)-Cyclobut-1-Enylamino]-Heptanoic Acid Hydroxyamide


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 Human HDAC2 in Complex with (R)-6-[3,4-Dioxo-2- (4-Trifluoromethoxy-Phenylamino)-Cyclobut-1-Enylamino]-Heptanoic Acid Hydroxyamide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F1004

b:78.2
occ:1.00
 F27 A:EL81004 0.0 78.2 1.0
C26 A:EL81004 1.3 74.6 1.0
F29 A:EL81004 2.2 75.6 1.0
F28 A:EL81004 2.2 71.4 1.0
O25 A:EL81004 2.3 72.0 1.0
O A:GLN31 3.1 63.7 1.0
C22 A:EL81004 3.6 64.2 1.0
O A:HOH1231 3.6 71.4 1.0
C A:GLY32 3.9 60.2 1.0
CA A:GLY32 4.0 57.9 1.0
C A:GLN31 4.2 63.2 1.0
N A:HIS33 4.2 54.4 1.0
O A:GLY32 4.3 59.3 1.0
C23 A:EL81004 4.4 60.2 1.0
C21 A:EL81004 4.4 60.6 1.0
N A:GLY32 4.5 58.8 1.0
O A:HOH1188 4.9 55.3 1.0
CA A:HIS33 5.0 50.9 1.0

Fluorine binding site 2 out of 9 in 6g3o

Go back to Fluorine Binding Sites List in 6g3o
Fluorine binding site 2 out of 9 in the Crystal Structure of Human HDAC2 in Complex with (R)-6-[3,4-Dioxo-2- (4-Trifluoromethoxy-Phenylamino)-Cyclobut-1-Enylamino]-Heptanoic Acid Hydroxyamide


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 Human HDAC2 in Complex with (R)-6-[3,4-Dioxo-2- (4-Trifluoromethoxy-Phenylamino)-Cyclobut-1-Enylamino]-Heptanoic Acid Hydroxyamide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F1004

b:71.4
occ:1.00
 F28 A:EL81004 0.0 71.4 1.0
C26 A:EL81004 1.3 74.6 1.0
F29 A:EL81004 2.2 75.6 1.0
O25 A:EL81004 2.2 72.0 1.0
F27 A:EL81004 2.2 78.2 1.0
C22 A:EL81004 2.6 64.2 1.0
C21 A:EL81004 3.3 60.6 1.0
C23 A:EL81004 3.4 60.2 1.0
C20 A:EL81004 4.3 56.6 1.0
C24 A:EL81004 4.4 56.4 1.0
OE2 A:GLU103 4.7 0.7 1.0
C19 A:EL81004 4.8 54.6 1.0

Fluorine binding site 3 out of 9 in 6g3o

Go back to Fluorine Binding Sites List in 6g3o
Fluorine binding site 3 out of 9 in the Crystal Structure of Human HDAC2 in Complex with (R)-6-[3,4-Dioxo-2- (4-Trifluoromethoxy-Phenylamino)-Cyclobut-1-Enylamino]-Heptanoic Acid Hydroxyamide


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 Human HDAC2 in Complex with (R)-6-[3,4-Dioxo-2- (4-Trifluoromethoxy-Phenylamino)-Cyclobut-1-Enylamino]-Heptanoic Acid Hydroxyamide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F1004

b:75.6
occ:1.00
 F29 A:EL81004 0.0 75.6 1.0
C26 A:EL81004 1.3 74.6 1.0
F27 A:EL81004 2.2 78.2 1.0
F28 A:EL81004 2.2 71.4 1.0
O25 A:EL81004 2.2 72.0 1.0
C22 A:EL81004 2.9 64.2 1.0
C23 A:EL81004 3.0 60.2 1.0
O A:HOH1188 3.4 55.3 1.0
C21 A:EL81004 4.2 60.6 1.0
O A:GLN31 4.2 63.7 1.0
C24 A:EL81004 4.3 56.4 1.0
OE2 A:GLU103 4.6 0.7 1.0
N A:HIS33 4.6 54.4 1.0
CA A:HIS33 4.7 50.9 1.0
CB A:HIS33 4.8 50.5 1.0
CD2 A:HIS33 4.8 53.2 1.0
C A:GLY32 4.8 60.2 1.0
O A:GLU103 5.0 76.1 1.0

Fluorine binding site 4 out of 9 in 6g3o

Go back to Fluorine Binding Sites List in 6g3o
Fluorine binding site 4 out of 9 in the Crystal Structure of Human HDAC2 in Complex with (R)-6-[3,4-Dioxo-2- (4-Trifluoromethoxy-Phenylamino)-Cyclobut-1-Enylamino]-Heptanoic Acid Hydroxyamide


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 Human HDAC2 in Complex with (R)-6-[3,4-Dioxo-2- (4-Trifluoromethoxy-Phenylamino)-Cyclobut-1-Enylamino]-Heptanoic Acid Hydroxyamide within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F1004

b:67.8
occ:1.00
 F27 B:EL81004 0.0 67.8 1.0
C26 B:EL81004 1.3 62.5 1.0
F29 B:EL81004 2.1 65.4 1.0
F28 B:EL81004 2.1 61.1 1.0
O25 B:EL81004 2.2 56.2 1.0
O B:GLN31 2.9 49.4 1.0
CA B:GLY32 3.5 42.7 1.0
C B:GLY32 3.5 43.9 1.0
C22 B:EL81004 3.6 52.3 1.0
C B:GLN31 3.8 49.5 1.0
O B:GLY32 3.9 43.6 1.0
N B:HIS33 3.9 38.0 1.0
N B:GLY32 4.1 44.8 1.0
C23 B:EL81004 4.4 49.4 1.0
C21 B:EL81004 4.5 48.6 1.0
CA B:HIS33 4.7 36.2 1.0
O B:HOH1141 4.7 58.9 1.0

Fluorine binding site 5 out of 9 in 6g3o

Go back to Fluorine Binding Sites List in 6g3o
Fluorine binding site 5 out of 9 in the Crystal Structure of Human HDAC2 in Complex with (R)-6-[3,4-Dioxo-2- (4-Trifluoromethoxy-Phenylamino)-Cyclobut-1-Enylamino]-Heptanoic Acid Hydroxyamide


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 Human HDAC2 in Complex with (R)-6-[3,4-Dioxo-2- (4-Trifluoromethoxy-Phenylamino)-Cyclobut-1-Enylamino]-Heptanoic Acid Hydroxyamide within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F1004

b:61.1
occ:1.00
 F28 B:EL81004 0.0 61.1 1.0
C26 B:EL81004 1.3 62.5 1.0
F27 B:EL81004 2.1 67.8 1.0
O25 B:EL81004 2.2 56.2 1.0
F29 B:EL81004 2.2 65.4 1.0
C22 B:EL81004 2.9 52.3 1.0
C23 B:EL81004 3.2 49.4 1.0
C21 B:EL81004 4.1 48.6 1.0
C24 B:EL81004 4.5 48.7 1.0
O B:GLN31 4.5 49.4 1.0
O B:HOH1172 4.8 45.8 1.0

Fluorine binding site 6 out of 9 in 6g3o

Go back to Fluorine Binding Sites List in 6g3o
Fluorine binding site 6 out of 9 in the Crystal Structure of Human HDAC2 in Complex with (R)-6-[3,4-Dioxo-2- (4-Trifluoromethoxy-Phenylamino)-Cyclobut-1-Enylamino]-Heptanoic Acid Hydroxyamide


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 Human HDAC2 in Complex with (R)-6-[3,4-Dioxo-2- (4-Trifluoromethoxy-Phenylamino)-Cyclobut-1-Enylamino]-Heptanoic Acid Hydroxyamide within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F1004

b:65.4
occ:1.00
 F29 B:EL81004 0.0 65.4 1.0
C26 B:EL81004 1.3 62.5 1.0
F27 B:EL81004 2.1 67.8 1.0
F28 B:EL81004 2.2 61.1 1.0
O25 B:EL81004 2.2 56.2 1.0
C22 B:EL81004 2.8 52.3 1.0
C23 B:EL81004 3.0 49.4 1.0
N B:HIS33 3.2 38.0 1.0
O B:GLN31 3.3 49.4 1.0
O B:HOH1172 3.4 45.8 1.0
CA B:HIS33 3.4 36.2 1.0
C B:GLY32 3.6 43.9 1.0
CB B:HIS33 3.6 35.9 1.0
O B:GLY32 4.0 43.6 1.0
C21 B:EL81004 4.1 48.6 1.0
CA B:GLY32 4.2 42.7 1.0
C B:GLN31 4.2 49.5 1.0
CG B:HIS33 4.3 38.2 1.0
CD2 B:HIS33 4.3 39.0 1.0
C24 B:EL81004 4.3 48.7 1.0
N B:GLY32 4.6 44.8 1.0
O B:GLY30 4.8 43.5 1.0
C B:HIS33 4.9 39.1 1.0

Fluorine binding site 7 out of 9 in 6g3o

Go back to Fluorine Binding Sites List in 6g3o
Fluorine binding site 7 out of 9 in the Crystal Structure of Human HDAC2 in Complex with (R)-6-[3,4-Dioxo-2- (4-Trifluoromethoxy-Phenylamino)-Cyclobut-1-Enylamino]-Heptanoic Acid Hydroxyamide


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 Human HDAC2 in Complex with (R)-6-[3,4-Dioxo-2- (4-Trifluoromethoxy-Phenylamino)-Cyclobut-1-Enylamino]-Heptanoic Acid Hydroxyamide within 5.0Å range:
probe atom residue distance (Å) B Occ
C:F1004

b:94.9
occ:1.00
 F27 C:EL81004 0.0 94.9 1.0
C26 C:EL81004 1.3 91.3 1.0
F28 C:EL81004 2.2 94.4 1.0
F29 C:EL81004 2.2 89.5 1.0
O25 C:EL81004 2.3 86.2 1.0
O C:GLN31 2.7 70.0 1.0
C22 C:EL81004 3.6 79.8 1.0
CA C:GLY32 3.6 66.0 1.0
C C:GLY32 3.6 67.6 1.0
C C:GLN31 3.7 71.0 1.0
N C:HIS33 3.8 61.4 1.0
N C:GLY32 4.1 66.9 1.0
O C:GLY32 4.1 67.8 1.0
C21 C:EL81004 4.4 77.4 1.0
C23 C:EL81004 4.4 73.7 1.0
CA C:HIS33 4.6 56.8 1.0

Fluorine binding site 8 out of 9 in 6g3o

Go back to Fluorine Binding Sites List in 6g3o
Fluorine binding site 8 out of 9 in the Crystal Structure of Human HDAC2 in Complex with (R)-6-[3,4-Dioxo-2- (4-Trifluoromethoxy-Phenylamino)-Cyclobut-1-Enylamino]-Heptanoic Acid Hydroxyamide


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 Human HDAC2 in Complex with (R)-6-[3,4-Dioxo-2- (4-Trifluoromethoxy-Phenylamino)-Cyclobut-1-Enylamino]-Heptanoic Acid Hydroxyamide within 5.0Å range:
probe atom residue distance (Å) B Occ
C:F1004

b:94.4
occ:1.00
 F28 C:EL81004 0.0 94.4 1.0
C26 C:EL81004 1.3 91.3 1.0
F27 C:EL81004 2.2 94.9 1.0
O25 C:EL81004 2.2 86.2 1.0
F29 C:EL81004 2.2 89.5 1.0
C22 C:EL81004 2.7 79.8 1.0
C21 C:EL81004 3.3 77.4 1.0
C23 C:EL81004 3.7 73.7 1.0
C20 C:EL81004 4.4 72.8 1.0
C24 C:EL81004 4.8 69.0 1.0
O C:GLN31 4.8 70.0 1.0
O C:GLY32 4.9 67.8 1.0
C C:GLY32 4.9 67.6 1.0

Fluorine binding site 9 out of 9 in 6g3o

Go back to Fluorine Binding Sites List in 6g3o
Fluorine binding site 9 out of 9 in the Crystal Structure of Human HDAC2 in Complex with (R)-6-[3,4-Dioxo-2- (4-Trifluoromethoxy-Phenylamino)-Cyclobut-1-Enylamino]-Heptanoic Acid Hydroxyamide


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 9 of Crystal Structure of Human HDAC2 in Complex with (R)-6-[3,4-Dioxo-2- (4-Trifluoromethoxy-Phenylamino)-Cyclobut-1-Enylamino]-Heptanoic Acid Hydroxyamide within 5.0Å range:
probe atom residue distance (Å) B Occ
C:F1004

b:89.5
occ:1.00
 F29 C:EL81004 0.0 89.5 1.0
C26 C:EL81004 1.3 91.3 1.0
F27 C:EL81004 2.2 94.9 1.0
F28 C:EL81004 2.2 94.4 1.0
O25 C:EL81004 2.2 86.2 1.0
C22 C:EL81004 2.9 79.8 1.0
C23 C:EL81004 3.0 73.7 1.0
C21 C:EL81004 4.1 77.4 1.0
O C:GLN31 4.2 70.0 1.0
C24 C:EL81004 4.4 69.0 1.0
N C:HIS33 4.7 61.4 1.0
CA C:HIS33 4.8 56.8 1.0
CB C:HIS33 4.9 55.5 1.0
CD2 C:HIS33 4.9 57.8 1.0
C C:GLY32 5.0 67.6 1.0

Reference:

J.F.Fournier, Y.Bhurruth-Alcor, B.Musicki, J.Aubert, M.Aurelly, C.Bouix-Peter, K.Bouquet, L.Chantalat, M.Delorme, B.Drean, G.Duvert, N.Fleury-Bregeot, B.Gauthier, K.Grisendi, C.S.Harris, L.F.Hennequin, T.Isabet, F.Joly, G.Lafitte, C.Millois, R.Morgentin, J.Pascau, D.Piwnica, Y.Rival, C.Soulet, E.Thoreau, L.Tomas. Squaramides As Novel Class I and Iib Histone Deacetylase Inhibitors For Topical Treatment of Cutaneous T-Cell Lymphoma. Bioorg. Med. Chem. Lett. V. 28 2985 2018.
ISSN: ESSN 1464-3405
PubMed: 30122227
DOI: 10.1016/J.BMCL.2018.06.029
Page generated: Tue Jul 15 11:45:18 2025

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