Atomistry » Fluorine » PDB 6g0l-6gpx » 6g3o
Atomistry »
  Fluorine »
    PDB 6g0l-6gpx »
      6g3o »

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: Thu Aug 1 20:23:41 2024

Last articles

Zn in 9J0N
Zn in 9J0O
Zn in 9J0P
Zn in 9FJX
Zn in 9EKB
Zn in 9C0F
Zn in 9CAH
Zn in 9CH0
Zn in 9CH3
Zn in 9CH1
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy