Fluorine in PDB 7kbg: Structure of Human HDAC2 in Complex with A 2-Substituted Benzamide Inhibitor (Compound 20)

Enzymatic activity of Structure of Human HDAC2 in Complex with A 2-Substituted Benzamide Inhibitor (Compound 20)

All present enzymatic activity of Structure of Human HDAC2 in Complex with A 2-Substituted Benzamide Inhibitor (Compound 20):
3.5.1.98;

Protein crystallography data

The structure of Structure of Human HDAC2 in Complex with A 2-Substituted Benzamide Inhibitor (Compound 20), PDB code: 7kbg was solved by D.J.Klein, J.Liu, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 25.08 / 1.26
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 92.26, 99.27, 139.02, 90, 90, 90
R / Rfree (%) 18.4 / 19.6

Other elements in 7kbg:

The structure of Structure of Human HDAC2 in Complex with A 2-Substituted Benzamide Inhibitor (Compound 20) also contains other interesting chemical elements:

Calcium (Ca) 6 atoms
Zinc (Zn) 3 atoms
Chlorine (Cl) 2 atoms

Fluorine Binding Sites:

The binding sites of Fluorine atom in the Structure of Human HDAC2 in Complex with A 2-Substituted Benzamide Inhibitor (Compound 20) (pdb code 7kbg). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 3 binding sites of Fluorine where determined in the Structure of Human HDAC2 in Complex with A 2-Substituted Benzamide Inhibitor (Compound 20), PDB code: 7kbg:
Jump to Fluorine binding site number: 1; 2; 3;

Fluorine binding site 1 out of 3 in 7kbg

Go back to Fluorine Binding Sites List in 7kbg
Fluorine binding site 1 out of 3 in the Structure of Human HDAC2 in Complex with A 2-Substituted Benzamide Inhibitor (Compound 20)


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of Structure of Human HDAC2 in Complex with A 2-Substituted Benzamide Inhibitor (Compound 20) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F411

b:13.0
occ:1.00
 F A:WBA411 0.0 13.0 1.0
C28 A:WBA411 1.4 12.5 1.0
C27 A:WBA411 2.3 13.3 1.0
C23 A:WBA411 2.4 12.3 1.0
C22 A:WBA411 2.9 12.2 1.0
N4 A:WBA411 3.0 13.1 1.0
O A:GLY150 3.0 13.3 1.0
CE A:MET31 3.0 16.4 1.0
OH A:TYR304 3.1 14.2 1.0
CB A:PHE151 3.2 12.4 1.0
CD2 A:PHE151 3.2 13.4 1.0
C26 A:WBA411 3.6 12.9 1.0
CG A:PHE151 3.6 12.6 1.0
C24 A:WBA411 3.6 12.6 1.0
O2 A:WBA411 3.9 12.4 1.0
C25 A:WBA411 4.1 12.9 1.0
C A:GLY150 4.1 13.1 1.0
C21 A:WBA411 4.2 14.3 1.0
CA A:PHE151 4.2 12.8 1.0
SG A:CYS152 4.3 13.3 1.0
CE2 A:PHE151 4.4 13.5 1.0
C A:PHE151 4.4 13.6 1.0
CZ A:TYR304 4.4 12.8 1.0
O A:PHE151 4.5 13.6 1.0
N A:PHE151 4.6 13.3 1.0
O1 A:WBA411 4.7 13.1 1.0
SD A:MET31 4.8 14.6 1.0
CA A:GLY302 4.9 11.9 1.0
N A:CYS152 4.9 12.8 1.0
CD1 A:PHE151 4.9 12.9 1.0
C20 A:WBA411 4.9 14.2 1.0
CE1 A:TYR304 4.9 12.8 1.0
CG A:MET31 5.0 15.3 1.0

Fluorine binding site 2 out of 3 in 7kbg

Go back to Fluorine Binding Sites List in 7kbg
Fluorine binding site 2 out of 3 in the Structure of Human HDAC2 in Complex with A 2-Substituted Benzamide Inhibitor (Compound 20)


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of Structure of Human HDAC2 in Complex with A 2-Substituted Benzamide Inhibitor (Compound 20) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F409

b:11.8
occ:1.00
 F B:WBA409 0.0 11.8 1.0
C28 B:WBA409 1.4 11.5 1.0
C27 B:WBA409 2.3 11.5 1.0
C23 B:WBA409 2.3 10.6 1.0
C22 B:WBA409 2.9 10.9 1.0
N4 B:WBA409 3.0 11.8 1.0
CE B:MET31 3.0 18.1 1.0
OH B:TYR304 3.1 13.0 1.0
O B:GLY150 3.1 11.5 1.0
CD2 B:PHE151 3.2 12.1 1.0
CB B:PHE151 3.2 12.1 1.0
C26 B:WBA409 3.6 11.2 1.0
CG B:PHE151 3.6 11.9 1.0
C24 B:WBA409 3.6 10.8 1.0
O2 B:WBA409 3.8 10.6 1.0
C25 B:WBA409 4.1 11.0 1.0
C B:GLY150 4.2 11.9 1.0
C21 B:WBA409 4.2 12.0 1.0
CA B:PHE151 4.3 12.3 1.0
SG B:CYS152 4.3 11.9 1.0
CE2 B:PHE151 4.3 13.2 1.0
CZ B:TYR304 4.4 11.7 1.0
C B:PHE151 4.4 12.0 1.0
O B:PHE151 4.6 12.6 1.0
N B:PHE151 4.6 11.9 1.0
SD B:MET31 4.7 14.6 1.0
O1 B:WBA409 4.7 10.6 1.0
CA B:GLY302 4.8 10.6 1.0
CE1 B:TYR304 4.9 11.9 1.0
CD1 B:PHE151 4.9 12.7 1.0
C20 B:WBA409 4.9 12.6 1.0
N B:CYS152 4.9 11.5 1.0
CG B:MET31 5.0 13.4 1.0

Fluorine binding site 3 out of 3 in 7kbg

Go back to Fluorine Binding Sites List in 7kbg
Fluorine binding site 3 out of 3 in the Structure of Human HDAC2 in Complex with A 2-Substituted Benzamide Inhibitor (Compound 20)


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of Structure of Human HDAC2 in Complex with A 2-Substituted Benzamide Inhibitor (Compound 20) within 5.0Å range:
probe atom residue distance (Å) B Occ
C:F412

b:13.8
occ:1.00
 F C:WBA412 0.0 13.8 1.0
C28 C:WBA412 1.4 12.8 1.0
C27 C:WBA412 2.3 12.8 1.0
C23 C:WBA412 2.4 12.6 1.0
C22 C:WBA412 2.9 13.5 1.0
N4 C:WBA412 3.0 14.4 1.0
O C:GLY150 3.1 13.8 1.0
OH C:TYR304 3.1 17.2 1.0
CE C:MET31 3.1 19.8 1.0
CD2 C:PHE151 3.2 14.2 1.0
CB C:PHE151 3.3 13.4 1.0
C26 C:WBA412 3.6 12.8 1.0
C24 C:WBA412 3.6 12.5 1.0
CG C:PHE151 3.6 13.6 1.0
O2 C:WBA412 3.8 13.7 1.0
C25 C:WBA412 4.1 12.6 1.0
C21 C:WBA412 4.2 14.5 1.0
C C:GLY150 4.2 13.4 1.0
CA C:PHE151 4.3 13.2 1.0
SG C:CYS152 4.3 13.2 1.0
CE2 C:PHE151 4.4 15.1 1.0
CZ C:TYR304 4.4 16.4 1.0
C C:PHE151 4.4 13.6 1.0
O C:PHE151 4.5 13.9 1.0
N C:PHE151 4.7 13.5 1.0
O1 C:WBA412 4.7 13.0 1.0
SD C:MET31 4.8 18.1 1.0
CA C:GLY302 4.8 13.6 1.0
C20 C:WBA412 4.9 15.0 1.0
CD1 C:PHE151 4.9 14.3 1.0
CE1 C:TYR304 4.9 16.2 1.0
N C:CYS152 4.9 13.0 1.0
CG C:MET31 4.9 18.0 1.0

Reference:

J.Liu, Y.Yu, J.Kelly, D.Sha, A.B.Alhassan, W.Yu, M.M.Maletic, J.L.Duffy, D.J.Klein, M.K.Holloway, S.Carroll, B.J.Howell, R.J.O.Barnard, S.Wolkenberg, J.A.Kozlowski. Discovery of Highly Selective and Potent HDAC3 Inhibitors Based on A 2-Substituted Benzamide Zinc Binding Group. Acs Med.Chem.Lett. V. 11 2476 2020.
ISSN: ISSN 1948-5875
PubMed: 33335670
DOI: 10.1021/ACSMEDCHEMLETT.0C00462
Page generated: Fri Aug 2 08:18:05 2024

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