Fluorine in PDB 5u7r: Identification of A New Class of Potent CDC7 Inhibitors Designed By Putative Pharmacophore Model: Synthesis and Biological Evaluation of 2,3-Dihydrothieno[3,2-D]Pyrimidin-4(1H)-Ones

Enzymatic activity of Identification of A New Class of Potent CDC7 Inhibitors Designed By Putative Pharmacophore Model: Synthesis and Biological Evaluation of 2,3-Dihydrothieno[3,2-D]Pyrimidin-4(1H)-Ones

All present enzymatic activity of Identification of A New Class of Potent CDC7 Inhibitors Designed By Putative Pharmacophore Model: Synthesis and Biological Evaluation of 2,3-Dihydrothieno[3,2-D]Pyrimidin-4(1H)-Ones:
2.7.11.1;

Protein crystallography data

The structure of Identification of A New Class of Potent CDC7 Inhibitors Designed By Putative Pharmacophore Model: Synthesis and Biological Evaluation of 2,3-Dihydrothieno[3,2-D]Pyrimidin-4(1H)-Ones, PDB code: 5u7r was solved by I.D.Hoffman, R.J.Skene, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 49.40 / 3.33
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 90.201, 146.137, 110.901, 90.00, 96.03, 90.00
R / Rfree (%) 20 / 24.1

Fluorine Binding Sites:

The binding sites of Fluorine atom in the Identification of A New Class of Potent CDC7 Inhibitors Designed By Putative Pharmacophore Model: Synthesis and Biological Evaluation of 2,3-Dihydrothieno[3,2-D]Pyrimidin-4(1H)-Ones (pdb code 5u7r). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 4 binding sites of Fluorine where determined in the Identification of A New Class of Potent CDC7 Inhibitors Designed By Putative Pharmacophore Model: Synthesis and Biological Evaluation of 2,3-Dihydrothieno[3,2-D]Pyrimidin-4(1H)-Ones, PDB code: 5u7r:
Jump to Fluorine binding site number: 1; 2; 3; 4;

Fluorine binding site 1 out of 4 in 5u7r

Go back to Fluorine Binding Sites List in 5u7r
Fluorine binding site 1 out of 4 in the Identification of A New Class of Potent CDC7 Inhibitors Designed By Putative Pharmacophore Model: Synthesis and Biological Evaluation of 2,3-Dihydrothieno[3,2-D]Pyrimidin-4(1H)-Ones


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of Identification of A New Class of Potent CDC7 Inhibitors Designed By Putative Pharmacophore Model: Synthesis and Biological Evaluation of 2,3-Dihydrothieno[3,2-D]Pyrimidin-4(1H)-Ones within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F500

b:0.3
occ:1.00
 F23 A:81G500 0.0 0.3 1.0
C22 A:81G500 1.4 0.5 1.0
C24 A:81G500 2.4 0.6 1.0
C21 A:81G500 2.4 0.9 1.0
C25 A:81G500 3.6 0.8 1.0
C20 A:81G500 3.6 0.8 1.0
CG1 A:VAL178 3.8 0.1 1.0
C19 A:81G500 4.1 0.9 1.0
OD1 A:ASP218 4.5 0.2 1.0
CG A:ASP218 4.8 0.8 1.0
CB A:VAL178 4.8 0.3 1.0

Fluorine binding site 2 out of 4 in 5u7r

Go back to Fluorine Binding Sites List in 5u7r
Fluorine binding site 2 out of 4 in the Identification of A New Class of Potent CDC7 Inhibitors Designed By Putative Pharmacophore Model: Synthesis and Biological Evaluation of 2,3-Dihydrothieno[3,2-D]Pyrimidin-4(1H)-Ones


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of Identification of A New Class of Potent CDC7 Inhibitors Designed By Putative Pharmacophore Model: Synthesis and Biological Evaluation of 2,3-Dihydrothieno[3,2-D]Pyrimidin-4(1H)-Ones within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F500

b:0.6
occ:1.00
 F23 B:81G500 0.0 0.6 1.0
C22 B:81G500 1.4 0.2 1.0
C24 B:81G500 2.4 0.2 1.0
C21 B:81G500 2.4 0.8 1.0
C25 B:81G500 3.6 0.1 1.0
C20 B:81G500 3.7 0.4 1.0
C19 B:81G500 4.1 0.7 1.0
OD2 B:ASP218 4.3 0.8 1.0
CG1 B:VAL178 4.4 0.4 1.0
OD2 B:ASP176 4.8 0.2 1.0

Fluorine binding site 3 out of 4 in 5u7r

Go back to Fluorine Binding Sites List in 5u7r
Fluorine binding site 3 out of 4 in the Identification of A New Class of Potent CDC7 Inhibitors Designed By Putative Pharmacophore Model: Synthesis and Biological Evaluation of 2,3-Dihydrothieno[3,2-D]Pyrimidin-4(1H)-Ones


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of Identification of A New Class of Potent CDC7 Inhibitors Designed By Putative Pharmacophore Model: Synthesis and Biological Evaluation of 2,3-Dihydrothieno[3,2-D]Pyrimidin-4(1H)-Ones within 5.0Å range:
probe atom residue distance (Å) B Occ
C:F500

b:0.7
occ:1.00
 F23 C:81G500 0.0 0.7 1.0
C22 C:81G500 1.4 0.7 1.0
C24 C:81G500 2.4 0.1 1.0
C21 C:81G500 2.4 0.2 1.0
C25 C:81G500 3.6 0.0 1.0
C20 C:81G500 3.6 0.1 1.0
C19 C:81G500 4.1 0.2 1.0
OD2 C:ASP176 4.5 0.1 1.0
OD1 C:ASP218 4.8 0.3 1.0

Fluorine binding site 4 out of 4 in 5u7r

Go back to Fluorine Binding Sites List in 5u7r
Fluorine binding site 4 out of 4 in the Identification of A New Class of Potent CDC7 Inhibitors Designed By Putative Pharmacophore Model: Synthesis and Biological Evaluation of 2,3-Dihydrothieno[3,2-D]Pyrimidin-4(1H)-Ones


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 4 of Identification of A New Class of Potent CDC7 Inhibitors Designed By Putative Pharmacophore Model: Synthesis and Biological Evaluation of 2,3-Dihydrothieno[3,2-D]Pyrimidin-4(1H)-Ones within 5.0Å range:
probe atom residue distance (Å) B Occ
D:F500

b:0.8
occ:1.00
 F23 D:81G500 0.0 0.8 1.0
C22 D:81G500 1.3 0.1 1.0
C24 D:81G500 2.4 0.0 1.0
C21 D:81G500 2.4 0.5 1.0
C25 D:81G500 3.6 0.1 1.0
C20 D:81G500 3.7 0.2 1.0
C19 D:81G500 4.1 0.5 1.0
CG1 D:VAL178 4.2 0.3 1.0
OD2 D:ASP176 4.7 0.4 1.0

Reference:

O.Kurasawa, Y.Oguro, T.Miyazaki, M.Homma, K.Mori, K.Iwai, H.Hara, R.Skene, I.Hoffman, A.Ohashi, S.Yoshida, T.Ishikawa, N.Cho. Identification of A New Class of Potent CDC7 Inhibitors Designed By Putative Pharmacophore Model: Synthesis and Biological Evaluation of 2,3-Dihydrothieno[3,2-D]Pyrimidin-4(1H)-Ones. Bioorg. Med. Chem. V. 25 2133 2017.
ISSN: ESSN 1464-3391
PubMed: 28284870
DOI: 10.1016/J.BMC.2017.02.021
Page generated: Sun Dec 13 12:39:06 2020

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