Fluorine in PDB 3uxm: Structure Guided Development of Novel Thymidine Mimetics Targeting Pseudomonas Aeruginosa Thymidylate Kinase: From Hit to Lead Generation

Enzymatic activity of Structure Guided Development of Novel Thymidine Mimetics Targeting Pseudomonas Aeruginosa Thymidylate Kinase: From Hit to Lead Generation

All present enzymatic activity of Structure Guided Development of Novel Thymidine Mimetics Targeting Pseudomonas Aeruginosa Thymidylate Kinase: From Hit to Lead Generation:
2.7.4.9;

Protein crystallography data

The structure of Structure Guided Development of Novel Thymidine Mimetics Targeting Pseudomonas Aeruginosa Thymidylate Kinase: From Hit to Lead Generation, PDB code: 3uxm was solved by J.Y.Choi, M.S.Plummer, J.Starr, C.R.Desbonnet, H.H.Soutter, J.Chang, J.R.Miller, K.Dillman, A.A.Miller, W.R.Roush, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 24.60 / 1.95
Space group P 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 73.877, 41.544, 117.886, 90.00, 90.02, 90.00
R / Rfree (%) 17.5 / 23.6

Other elements in 3uxm:

The structure of Structure Guided Development of Novel Thymidine Mimetics Targeting Pseudomonas Aeruginosa Thymidylate Kinase: From Hit to Lead Generation also contains other interesting chemical elements:

Magnesium (Mg) 4 atoms

Fluorine Binding Sites:

The binding sites of Fluorine atom in the Structure Guided Development of Novel Thymidine Mimetics Targeting Pseudomonas Aeruginosa Thymidylate Kinase: From Hit to Lead Generation (pdb code 3uxm). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 4 binding sites of Fluorine where determined in the Structure Guided Development of Novel Thymidine Mimetics Targeting Pseudomonas Aeruginosa Thymidylate Kinase: From Hit to Lead Generation, PDB code: 3uxm:
Jump to Fluorine binding site number: 1; 2; 3; 4;

Fluorine binding site 1 out of 4 in 3uxm

Go back to Fluorine Binding Sites List in 3uxm
Fluorine binding site 1 out of 4 in the Structure Guided Development of Novel Thymidine Mimetics Targeting Pseudomonas Aeruginosa Thymidylate Kinase: From Hit to Lead Generation


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of Structure Guided Development of Novel Thymidine Mimetics Targeting Pseudomonas Aeruginosa Thymidylate Kinase: From Hit to Lead Generation within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F800

b:20.1
occ:1.00
 F1 A:0DN800 0.0 20.1 1.0
C5 A:0DN800 1.4 17.1 1.0
C1 A:0DN800 2.4 20.5 1.0
C2 A:0DN800 2.9 17.8 1.0
O1 A:0DN800 2.9 19.6 1.0
O A:HOH231 3.1 24.4 1.0
O A:GLU39 3.3 17.1 1.0
C3 A:0DN800 3.4 16.0 1.0
C4 A:0DN800 3.6 18.7 1.0
NH1 A:ARG50 3.6 16.0 1.0
C9 A:0DN800 3.7 14.5 1.0
CD A:ARG96 3.7 20.6 1.0
CD A:PRO40 3.7 16.3 1.0
NH2 A:ARG50 3.9 21.4 1.0
O A:HOH219 3.9 23.2 1.0
N1 A:0DN800 4.1 21.2 1.0
CZ A:ARG50 4.1 26.9 1.0
C A:GLU39 4.2 16.5 1.0
O2 A:0DN800 4.2 17.6 1.0
NE A:ARG96 4.3 26.7 1.0
N A:PRO40 4.4 16.8 1.0
CG A:ARG96 4.7 19.1 1.0
C8 A:0DN800 4.8 15.6 1.0
O A:HOH278 4.8 23.4 1.0
CG A:PRO40 4.8 17.1 1.0
CB A:ARG96 5.0 16.4 1.0

Fluorine binding site 2 out of 4 in 3uxm

Go back to Fluorine Binding Sites List in 3uxm
Fluorine binding site 2 out of 4 in the Structure Guided Development of Novel Thymidine Mimetics Targeting Pseudomonas Aeruginosa Thymidylate Kinase: From Hit to Lead Generation


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of Structure Guided Development of Novel Thymidine Mimetics Targeting Pseudomonas Aeruginosa Thymidylate Kinase: From Hit to Lead Generation within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F801

b:21.4
occ:1.00
 F1 B:0DN801 0.0 21.4 1.0
C5 B:0DN801 1.4 19.3 1.0
C1 B:0DN801 2.4 17.9 1.0
C2 B:0DN801 2.8 21.6 1.0
O1 B:0DN801 2.8 18.1 1.0
NH1 B:ARG96 3.2 20.7 1.0
C3 B:0DN801 3.3 19.8 1.0
O B:GLU39 3.3 16.8 1.0
O B:HOH278 3.3 17.3 1.0
O B:HOH256 3.4 26.2 1.0
C4 B:0DN801 3.6 19.9 1.0
CD B:PRO40 3.6 16.6 1.0
C9 B:0DN801 3.6 16.6 1.0
NH1 B:ARG50 3.8 18.0 1.0
CD B:ARG96 4.0 24.7 1.0
CZ B:ARG96 4.0 27.2 1.0
NH2 B:ARG50 4.0 19.3 1.0
N1 B:0DN801 4.1 17.0 1.0
C B:GLU39 4.2 17.6 1.0
O2 B:0DN801 4.2 20.4 1.0
CZ B:ARG50 4.2 20.5 1.0
NE B:ARG96 4.3 23.3 1.0
N B:PRO40 4.3 19.6 1.0
CG B:PRO40 4.7 16.1 1.0
C8 B:0DN801 4.8 17.6 1.0
CD1 B:LEU54 4.9 24.2 1.0
CG B:ARG96 5.0 23.5 1.0

Fluorine binding site 3 out of 4 in 3uxm

Go back to Fluorine Binding Sites List in 3uxm
Fluorine binding site 3 out of 4 in the Structure Guided Development of Novel Thymidine Mimetics Targeting Pseudomonas Aeruginosa Thymidylate Kinase: From Hit to Lead Generation


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of Structure Guided Development of Novel Thymidine Mimetics Targeting Pseudomonas Aeruginosa Thymidylate Kinase: From Hit to Lead Generation within 5.0Å range:
probe atom residue distance (Å) B Occ
C:F802

b:23.5
occ:1.00
 F1 C:0DN802 0.0 23.5 1.0
C5 C:0DN802 1.4 20.8 1.0
C1 C:0DN802 2.3 19.4 1.0
C2 C:0DN802 2.8 15.8 1.0
O1 C:0DN802 2.8 17.8 1.0
O C:HOH301 3.0 34.2 1.0
O C:HOH239 3.2 24.1 1.0
C3 C:0DN802 3.2 15.4 1.0
O C:GLU39 3.4 17.3 1.0
C4 C:0DN802 3.5 16.3 1.0
C9 C:0DN802 3.7 18.5 1.0
CD C:ARG96 3.7 25.8 1.0
NH1 C:ARG50 3.7 13.6 1.0
CD C:PRO40 3.8 12.2 1.0
O C:HOH256 3.8 22.1 1.0
NH2 C:ARG50 4.0 22.5 1.0
N1 C:0DN802 4.1 19.4 1.0
O2 C:0DN802 4.1 17.7 1.0
NE C:ARG96 4.2 24.5 1.0
CZ C:ARG50 4.2 21.4 1.0
C C:GLU39 4.4 14.3 1.0
N C:PRO40 4.5 15.4 1.0
O C:HOH277 4.7 19.9 1.0
C8 C:0DN802 4.8 14.6 1.0
CG C:ARG96 4.9 22.1 1.0
CG C:PRO40 4.9 14.0 1.0

Fluorine binding site 4 out of 4 in 3uxm

Go back to Fluorine Binding Sites List in 3uxm
Fluorine binding site 4 out of 4 in the Structure Guided Development of Novel Thymidine Mimetics Targeting Pseudomonas Aeruginosa Thymidylate Kinase: From Hit to Lead Generation


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 4 of Structure Guided Development of Novel Thymidine Mimetics Targeting Pseudomonas Aeruginosa Thymidylate Kinase: From Hit to Lead Generation within 5.0Å range:
probe atom residue distance (Å) B Occ
D:F803

b:21.2
occ:1.00
 F1 D:0DN803 0.0 21.2 1.0
C5 D:0DN803 1.4 16.2 1.0
C1 D:0DN803 2.3 18.7 1.0
O1 D:0DN803 2.8 15.9 1.0
C2 D:0DN803 2.9 21.9 1.0
O D:HOH257 3.2 16.7 1.0
NH1 D:ARG96 3.3 20.7 1.0
O D:GLU39 3.3 18.5 1.0
C3 D:0DN803 3.3 17.4 1.0
O D:HOH244 3.4 23.9 1.0
CD D:PRO40 3.5 13.9 1.0
C4 D:0DN803 3.6 18.6 1.0
C9 D:0DN803 3.6 15.1 1.0
NH1 D:ARG50 3.7 14.9 1.0
CD D:ARG96 3.9 24.4 1.0
CZ D:ARG96 4.0 28.4 1.0
N1 D:0DN803 4.1 17.8 1.0
C D:GLU39 4.2 17.3 1.0
O2 D:0DN803 4.2 23.3 1.0
NH2 D:ARG50 4.2 20.2 1.0
NE D:ARG96 4.2 23.4 1.0
N D:PRO40 4.3 17.9 1.0
CZ D:ARG50 4.3 20.3 1.0
CG D:PRO40 4.7 17.3 1.0
C8 D:0DN803 4.7 17.9 1.0
NH2 D:ARG96 4.9 22.8 1.0

Reference:

J.Y.Choi, M.S.Plummer, J.Starr, C.R.Desbonnet, H.Soutter, J.Chang, J.R.Miller, K.Dillman, A.A.Miller, W.R.Roush. Structure Guided Development of Novel Thymidine Mimetics Targeting Pseudomonas Aeruginosa Thymidylate Kinase: From Hit to Lead Generation. J.Med.Chem. V. 55 852 2012.
ISSN: ISSN 0022-2623
PubMed: 22243413
DOI: 10.1021/JM201349F
Page generated: Sun Dec 13 11:56:44 2020

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