Fluorine in PDB 6pye: Crystal Structure of Danio Rerio Histone Deacetylase 6 Catalytic Domain 2 Complexed with NR160

The structure of Crystal Structure of Danio Rerio Histone Deacetylase 6 Catalytic Domain 2 Complexed with NR160, PDB code: 6pye was solved by J.D.Osko, D.W.Christianson, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	60.32 / 1.48
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	55.000, 83.130, 88.590, 90.00, 98.33, 90.00
R / Rfree (%)	16.4 / 18.2

The structure of Crystal Structure of Danio Rerio Histone Deacetylase 6 Catalytic Domain 2 Complexed with NR160 also contains other interesting chemical elements:

Potassium	(K)	4 atoms
Zinc	(Zn)	2 atoms

The binding sites of Fluorine atom in the Crystal Structure of Danio Rerio Histone Deacetylase 6 Catalytic Domain 2 Complexed with NR160 (pdb code 6pye). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 6 binding sites of Fluorine where determined in the Crystal Structure of Danio Rerio Histone Deacetylase 6 Catalytic Domain 2 Complexed with NR160, PDB code: 6pye:
Jump to Fluorine binding site number: 1; 2; 3; 4; 5; 6;

Fluorine binding site 1 out of 6 in the Crystal Structure of Danio Rerio Histone Deacetylase 6 Catalytic Domain 2 Complexed with NR160


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 6 Catalytic Domain 2 Complexed with NR160 within 5.0Å range: probe atom residue distance (Å) B Occ A:F801 b:21.3 occ:0.91 F26 A:P5Y801 0.0 21.3 0.9 C25 A:P5Y801 1.3 19.7 0.9 F28 A:P5Y801 2.1 15.7 0.9 F27 A:P5Y801 2.1 18.2 0.9 C24 A:P5Y801 2.4 12.9 0.9 C29 A:P5Y801 2.8 15.5 0.9 O A:HOH1340 3.2 34.9 1.0 CD2 A:LEU712 3.3 22.9 1.0 C23 A:P5Y801 3.7 12.5 0.9 CG A:PRO464 3.7 14.1 1.0 CD1 A:LEU712 3.8 22.4 1.0 CG A:LEU712 4.1 17.1 1.0 C30 A:P5Y801 4.2 18.5 0.9 C22 A:P5Y801 4.3 12.1 0.9 CD A:PRO464 4.4 11.8 1.0 O33 A:P5Y801 4.5 16.3 0.9 CB A:PRO464 4.8 11.7 1.0 C32 A:P5Y801 4.8 15.0 0.9 C05 A:P5Y801 4.8 12.3 0.9 C31 A:P5Y801 5.0 15.3 0.9

Fluorine binding site 2 out of 6 in the Crystal Structure of Danio Rerio Histone Deacetylase 6 Catalytic Domain 2 Complexed with NR160


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 6 Catalytic Domain 2 Complexed with NR160 within 5.0Å range: probe atom residue distance (Å) B Occ A:F801 b:18.2 occ:0.91 F27 A:P5Y801 0.0 18.2 0.9 C25 A:P5Y801 1.4 19.7 0.9 F28 A:P5Y801 2.1 15.7 0.9 F26 A:P5Y801 2.1 21.3 0.9 C24 A:P5Y801 2.4 12.9 0.9 O33 A:P5Y801 3.1 16.3 0.9 C29 A:P5Y801 3.2 15.5 0.9 C23 A:P5Y801 3.2 12.5 0.9 O A:HOH963 3.3 18.2 1.0 C22 A:P5Y801 3.4 12.1 0.9 O A:HOH1340 4.1 34.9 1.0 CD2 A:LEU712 4.4 22.9 1.0 C32 A:P5Y801 4.5 15.0 0.9 C30 A:P5Y801 4.5 18.5 0.9 N08 A:P5Y801 4.7 14.5 0.9 N11 A:P5Y801 4.7 11.9 0.9 N12 A:P5Y801 4.7 14.3 0.9 C10 A:P5Y801 4.9 13.0 0.9 N13 A:P5Y801 4.9 12.5 0.9 C31 A:P5Y801 5.0 15.3 0.9

Fluorine binding site 3 out of 6 in the Crystal Structure of Danio Rerio Histone Deacetylase 6 Catalytic Domain 2 Complexed with NR160


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 6 Catalytic Domain 2 Complexed with NR160 within 5.0Å range: probe atom residue distance (Å) B Occ A:F801 b:15.7 occ:0.91 F28 A:P5Y801 0.0 15.7 0.9 C25 A:P5Y801 1.3 19.7 0.9 F26 A:P5Y801 2.1 21.3 0.9 F27 A:P5Y801 2.1 18.2 0.9 C24 A:P5Y801 2.5 12.9 0.9 C22 A:P5Y801 2.7 12.1 0.9 O33 A:P5Y801 2.9 16.3 0.9 C23 A:P5Y801 2.9 12.5 0.9 N11 A:P5Y801 3.3 11.9 0.9 N08 A:P5Y801 3.4 14.5 0.9 C05 A:P5Y801 3.5 12.3 0.9 C29 A:P5Y801 3.6 15.5 0.9 C10 A:P5Y801 3.7 13.0 0.9 CD2 A:LEU712 3.8 22.9 1.0 N12 A:P5Y801 3.8 14.3 0.9 CD1 A:LEU712 3.8 22.4 1.0 C07 A:P5Y801 4.1 13.9 0.9 C09 A:P5Y801 4.1 14.7 0.9 C06 A:P5Y801 4.2 11.0 0.9 C32 A:P5Y801 4.3 15.0 0.9 N14 A:P5Y801 4.3 13.9 0.9 N13 A:P5Y801 4.4 12.5 0.9 CG A:LEU712 4.4 17.1 1.0 C04 A:P5Y801 4.5 12.9 0.9 O A:HOH963 4.5 18.2 1.0 O A:HOH1072 4.8 11.1 1.0 C30 A:P5Y801 4.8 18.5 0.9

Fluorine binding site 4 out of 6 in the Crystal Structure of Danio Rerio Histone Deacetylase 6 Catalytic Domain 2 Complexed with NR160


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 Danio Rerio Histone Deacetylase 6 Catalytic Domain 2 Complexed with NR160 within 5.0Å range: probe atom residue distance (Å) B Occ B:F801 b:23.7 occ:0.94 F26 B:P5Y801 0.0 23.7 0.9 C25 B:P5Y801 1.3 19.8 0.9 F28 B:P5Y801 2.1 20.1 0.9 F27 B:P5Y801 2.1 21.4 0.9 C24 B:P5Y801 2.4 16.1 0.9 C29 B:P5Y801 2.8 16.8 0.9 CD2 B:LEU712 3.4 22.6 1.0 CG B:PRO464 3.6 16.0 1.0 C23 B:P5Y801 3.7 15.3 0.9 CD1 B:LEU712 3.8 18.7 1.0 CD B:PRO464 4.0 13.2 1.0 C30 B:P5Y801 4.1 19.8 0.9 CG B:LEU712 4.2 18.2 1.0 C22 B:P5Y801 4.3 19.7 0.9 O33 B:P5Y801 4.5 20.5 0.9 CB B:PRO464 4.6 13.9 1.0 C32 B:P5Y801 4.7 16.9 0.9 C05 B:P5Y801 4.9 16.8 0.9 C31 B:P5Y801 5.0 17.8 0.9

Fluorine binding site 5 out of 6 in the Crystal Structure of Danio Rerio Histone Deacetylase 6 Catalytic Domain 2 Complexed with NR160


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 Danio Rerio Histone Deacetylase 6 Catalytic Domain 2 Complexed with NR160 within 5.0Å range: probe atom residue distance (Å) B Occ B:F801 b:21.4 occ:0.94 F27 B:P5Y801 0.0 21.4 0.9 C25 B:P5Y801 1.4 19.8 0.9 F28 B:P5Y801 2.1 20.1 0.9 F26 B:P5Y801 2.1 23.7 0.9 C24 B:P5Y801 2.4 16.1 0.9 C22 B:P5Y801 2.7 19.7 0.9 C23 B:P5Y801 2.9 15.3 0.9 O33 B:P5Y801 2.9 20.5 0.9 N08 B:P5Y801 3.4 18.5 0.9 N11 B:P5Y801 3.5 17.7 0.9 C05 B:P5Y801 3.5 16.8 0.9 C29 B:P5Y801 3.6 16.8 0.9 CD2 B:LEU712 3.7 22.6 1.0 CD1 B:LEU712 3.7 18.7 1.0 C10 B:P5Y801 3.8 15.7 0.9 N12 B:P5Y801 4.0 23.2 0.9 C07 B:P5Y801 4.1 15.9 0.9 C09 B:P5Y801 4.1 19.2 0.9 C06 B:P5Y801 4.2 16.6 0.9 C32 B:P5Y801 4.3 16.9 0.9 CG B:LEU712 4.3 18.2 1.0 C04 B:P5Y801 4.5 15.6 0.9 N14 B:P5Y801 4.5 16.2 0.9 N13 B:P5Y801 4.6 20.6 0.9 O B:HOH1018 4.6 20.4 1.0 C30 B:P5Y801 4.8 19.8 0.9 O B:HOH1035 4.8 14.9 1.0

Fluorine binding site 6 out of 6 in the Crystal Structure of Danio Rerio Histone Deacetylase 6 Catalytic Domain 2 Complexed with NR160


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 Danio Rerio Histone Deacetylase 6 Catalytic Domain 2 Complexed with NR160 within 5.0Å range: probe atom residue distance (Å) B Occ B:F801 b:20.1 occ:0.94 F28 B:P5Y801 0.0 20.1 0.9 C25 B:P5Y801 1.3 19.8 0.9 F27 B:P5Y801 2.1 21.4 0.9 F26 B:P5Y801 2.1 23.7 0.9 C24 B:P5Y801 2.4 16.1 0.9 O33 B:P5Y801 3.1 20.5 0.9 C23 B:P5Y801 3.3 15.3 0.9 C29 B:P5Y801 3.3 16.8 0.9 O B:HOH1018 3.4 20.4 1.0 C22 B:P5Y801 3.4 19.7 0.9 CD2 B:LEU712 4.2 22.6 1.0 C32 B:P5Y801 4.5 16.9 0.9 C30 B:P5Y801 4.5 19.8 0.9 N08 B:P5Y801 4.7 18.5 0.9 N11 B:P5Y801 4.8 17.7 0.9 N12 B:P5Y801 4.8 23.2 0.9 C10 B:P5Y801 4.9 15.7 0.9

N.Ressing, M.Sonnichsen, J.D.Osko, A.Scholer, J.Schliehe-Diecks, A.Skerhut, A.Borkhardt, J.Hauer, M.U.Kassack, D.W.Christianson, S.Bhatia, F.K.Hansen. Multicomponent Synthesis, Binding Mode, and Structure-Activity Relationship of Selective Histone Deacetylase 6 (HDAC6) Inhibitors with Bifurcated Capping Groups. J.Med.Chem. V. 63 10339 2020.
ISSN: ISSN 0022-2623
PubMed: 32803970
DOI: 10.1021/ACS.JMEDCHEM.9B01888