Fluorine in PDB 4e28: Structure of Human Thymidylate Synthase in Inactive Conformation with A Novel Non-Peptidic Inhibitor

Enzymatic activity of Structure of Human Thymidylate Synthase in Inactive Conformation with A Novel Non-Peptidic Inhibitor

All present enzymatic activity of Structure of Human Thymidylate Synthase in Inactive Conformation with A Novel Non-Peptidic Inhibitor:
2.1.1.45;

Protein crystallography data

The structure of Structure of Human Thymidylate Synthase in Inactive Conformation with A Novel Non-Peptidic Inhibitor, PDB code: 4e28 was solved by A.Tochowicz, J.Finer-Moore, R.M.Stroud, M.P.Costi, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 29.23 / 2.30
Space group P 31 2 1
Cell size a, b, c (Å), α, β, γ (°) 95.747, 95.747, 82.407, 90.00, 90.00, 120.00
R / Rfree (%) 18.8 / 22.9

Fluorine Binding Sites:

The binding sites of Fluorine atom in the Structure of Human Thymidylate Synthase in Inactive Conformation with A Novel Non-Peptidic Inhibitor (pdb code 4e28). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 6 binding sites of Fluorine where determined in the Structure of Human Thymidylate Synthase in Inactive Conformation with A Novel Non-Peptidic Inhibitor, PDB code: 4e28:
Jump to Fluorine binding site number: 1; 2; 3; 4; 5; 6;

Fluorine binding site 1 out of 6 in 4e28

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Fluorine binding site 1 out of 6 in the Structure of Human Thymidylate Synthase in Inactive Conformation with A Novel Non-Peptidic Inhibitor


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 Thymidylate Synthase in Inactive Conformation with A Novel Non-Peptidic Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F403

b:0.7
occ:0.32
 F28 A:0MZ403 0.0 0.7 0.3
H24 A:9MZ404 1.2 1.0 0.7
C27 A:0MZ403 1.3 0.7 0.3
C24 A:9MZ404 1.6 0.9 0.7
F29 A:9MZ404 1.9 1.0 0.7
C25 A:9MZ404 2.0 0.5 0.7
F30 A:0MZ403 2.2 0.2 0.3
F29 A:0MZ403 2.2 0.1 0.3
C27 A:9MZ404 2.3 0.6 0.7
C25 A:0MZ403 2.3 0.1 0.3
H26 A:0MZ403 2.3 0.4 0.3
C26 A:0MZ403 2.7 0.6 0.3
C23 A:9MZ404 2.7 0.3 0.7
F30 A:9MZ404 2.8 0.8 0.7
H23 A:9MZ404 3.2 0.1 0.7
C26 A:9MZ404 3.3 0.6 0.7
F28 A:9MZ404 3.5 0.1 0.7
C24 A:0MZ403 3.6 0.5 0.3
C22 A:9MZ404 3.8 1.0 0.7
H24 A:0MZ403 4.0 0.5 0.3
C21 A:9MZ404 4.0 0.7 0.7
C21 A:0MZ403 4.0 0.9 0.3
H26 A:9MZ404 4.1 0.3 0.7
C23 A:0MZ403 4.7 0.4 0.3
H22 A:9MZ404 4.7 0.5 0.7
N18 A:0MZ403 4.9 0.5 0.3
C22 A:0MZ403 4.9 0.2 0.3

Fluorine binding site 2 out of 6 in 4e28

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Fluorine binding site 2 out of 6 in the Structure of Human Thymidylate Synthase in Inactive Conformation with A Novel Non-Peptidic Inhibitor


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 Thymidylate Synthase in Inactive Conformation with A Novel Non-Peptidic Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F403

b:0.2
occ:0.32
 F30 A:0MZ403 0.0 0.2 0.3
F29 A:9MZ404 0.9 1.0 0.7
C27 A:0MZ403 1.3 0.7 0.3
C27 A:9MZ404 1.4 0.6 0.7
F30 A:9MZ404 1.5 0.8 0.7
F28 A:0MZ403 2.2 0.7 0.3
F29 A:0MZ403 2.2 0.1 0.3
C25 A:0MZ403 2.3 0.1 0.3
F28 A:9MZ404 2.3 0.1 0.7
C25 A:9MZ404 2.6 0.5 0.7
H24 A:9MZ404 2.8 1.0 0.7
C24 A:0MZ403 3.0 0.5 0.3
H24 A:0MZ403 3.1 0.5 0.3
C24 A:9MZ404 3.1 0.9 0.7
C26 A:0MZ403 3.2 0.6 0.3
H26 A:0MZ403 3.4 0.4 0.3
O A:LEU101 3.6 0.1 1.0
C26 A:9MZ404 3.8 0.6 0.7
H26 A:9MZ404 4.0 0.3 0.7
C23 A:0MZ403 4.3 0.4 0.3
C23 A:9MZ404 4.4 0.3 0.7
C21 A:0MZ403 4.4 0.9 0.3
C A:LEU101 4.8 0.9 1.0
C22 A:0MZ403 4.9 0.2 0.3
C21 A:9MZ404 5.0 0.7 0.7

Fluorine binding site 3 out of 6 in 4e28

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Fluorine binding site 3 out of 6 in the Structure of Human Thymidylate Synthase in Inactive Conformation with A Novel Non-Peptidic Inhibitor


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 Thymidylate Synthase in Inactive Conformation with A Novel Non-Peptidic Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F403

b:0.1
occ:0.32
 F29 A:0MZ403 0.0 0.1 0.3
C27 A:0MZ403 1.3 0.7 0.3
H24 A:9MZ404 1.7 1.0 0.7
F30 A:9MZ404 1.9 0.8 0.7
F30 A:0MZ403 2.2 0.2 0.3
F28 A:0MZ403 2.2 0.7 0.3
C25 A:0MZ403 2.3 0.1 0.3
C24 A:9MZ404 2.4 0.9 0.7
H24 A:0MZ403 2.6 0.5 0.3
C27 A:9MZ404 2.6 0.6 0.7
F29 A:9MZ404 2.8 1.0 0.7
C24 A:0MZ403 2.8 0.5 0.3
C25 A:9MZ404 2.8 0.5 0.7
C26 A:0MZ403 3.5 0.6 0.3
C23 A:9MZ404 3.6 0.3 0.7
H26 A:0MZ403 3.8 0.4 0.3
F28 A:9MZ404 3.8 0.1 0.7
H23 A:9MZ404 4.0 0.1 0.7
C23 A:0MZ403 4.1 0.4 0.3
C26 A:9MZ404 4.2 0.6 0.7
C21 A:0MZ403 4.6 0.9 0.3
C22 A:9MZ404 4.8 1.0 0.7
H23 A:0MZ403 4.8 0.0 0.3
H26 A:9MZ404 4.8 0.3 0.7
C22 A:0MZ403 4.9 0.2 0.3
C21 A:9MZ404 5.0 0.7 0.7

Fluorine binding site 4 out of 6 in 4e28

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Fluorine binding site 4 out of 6 in the Structure of Human Thymidylate Synthase in Inactive Conformation with A Novel Non-Peptidic Inhibitor


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 4 of Structure of Human Thymidylate Synthase in Inactive Conformation with A Novel Non-Peptidic Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F404

b:0.1
occ:0.68
 F28 A:9MZ404 0.0 0.1 0.7
C27 A:9MZ404 1.3 0.6 0.7
F29 A:9MZ404 2.1 1.0 0.7
F30 A:9MZ404 2.2 0.8 0.7
C25 A:0MZ403 2.2 0.1 0.3
H26 A:9MZ404 2.3 0.3 0.7
C25 A:9MZ404 2.3 0.5 0.7
F30 A:0MZ403 2.3 0.2 0.3
C26 A:0MZ403 2.5 0.6 0.3
C24 A:0MZ403 2.6 0.5 0.3
C26 A:9MZ404 2.6 0.6 0.7
C27 A:0MZ403 2.7 0.7 0.3
H26 A:0MZ403 3.0 0.4 0.3
O A:LEU101 3.1 0.1 1.0
H24 A:0MZ403 3.1 0.5 0.3
C21 A:0MZ403 3.1 0.9 0.3
C23 A:0MZ403 3.2 0.4 0.3
C22 A:0MZ403 3.4 0.2 0.3
F28 A:0MZ403 3.5 0.7 0.3
C24 A:9MZ404 3.6 0.9 0.7
F29 A:0MZ403 3.8 0.1 0.3
CG A:LEU101 3.8 98.2 1.0
H24 A:9MZ404 4.0 1.0 0.7
H23 A:0MZ403 4.0 0.0 0.3
C21 A:9MZ404 4.0 0.7 0.7
CD2 A:LEU101 4.0 95.0 1.0
O19 A:9MZ404 4.1 0.8 0.7
N18 A:0MZ403 4.1 0.5 0.3
C A:LEU101 4.3 0.9 1.0
H22 A:0MZ403 4.3 0.5 0.3
CB A:LEU101 4.5 0.7 1.0
C23 A:9MZ404 4.7 0.3 0.7
C22 A:9MZ404 4.9 1.0 0.7
C17 A:9MZ404 4.9 0.7 0.7
N18 A:9MZ404 4.9 0.3 0.7
CD1 A:LEU101 4.9 94.1 1.0

Fluorine binding site 5 out of 6 in 4e28

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Fluorine binding site 5 out of 6 in the Structure of Human Thymidylate Synthase in Inactive Conformation with A Novel Non-Peptidic Inhibitor


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 5 of Structure of Human Thymidylate Synthase in Inactive Conformation with A Novel Non-Peptidic Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F404

b:0.8
occ:0.68
 F30 A:9MZ404 0.0 0.8 0.7
C27 A:9MZ404 1.3 0.6 0.7
C27 A:0MZ403 1.5 0.7 0.3
F30 A:0MZ403 1.5 0.2 0.3
H24 A:0MZ403 1.5 0.5 0.3
C25 A:0MZ403 1.6 0.1 0.3
C24 A:0MZ403 1.6 0.5 0.3
F29 A:0MZ403 1.9 0.1 0.3
F28 A:9MZ404 2.2 0.1 0.7
F29 A:9MZ404 2.2 1.0 0.7
C25 A:9MZ404 2.3 0.5 0.7
F28 A:0MZ403 2.8 0.7 0.3
H24 A:9MZ404 2.8 1.0 0.7
C26 A:0MZ403 2.9 0.6 0.3
C24 A:9MZ404 2.9 0.9 0.7
C23 A:0MZ403 3.0 0.4 0.3
C26 A:9MZ404 3.4 0.6 0.7
H26 A:0MZ403 3.5 0.4 0.3
H26 A:9MZ404 3.6 0.3 0.7
H23 A:0MZ403 3.6 0.0 0.3
O A:LEU101 3.6 0.1 1.0
C21 A:0MZ403 3.8 0.9 0.3
C22 A:0MZ403 3.8 0.2 0.3
C23 A:9MZ404 4.2 0.3 0.7
C21 A:9MZ404 4.5 0.7 0.7
CA A:SER102 4.8 0.3 1.0
C A:LEU101 4.8 0.9 1.0
H22 A:0MZ403 4.8 0.5 0.3
C22 A:9MZ404 4.9 1.0 0.7
H23 A:9MZ404 5.0 0.1 0.7

Fluorine binding site 6 out of 6 in 4e28

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Fluorine binding site 6 out of 6 in the Structure of Human Thymidylate Synthase in Inactive Conformation with A Novel Non-Peptidic Inhibitor


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 6 of Structure of Human Thymidylate Synthase in Inactive Conformation with A Novel Non-Peptidic Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F404

b:1.0
occ:0.68
 F29 A:9MZ404 0.0 1.0 0.7
F30 A:0MZ403 0.9 0.2 0.3
C27 A:9MZ404 1.3 0.6 0.7
C27 A:0MZ403 1.6 0.7 0.3
F28 A:0MZ403 1.9 0.7 0.3
F28 A:9MZ404 2.1 0.1 0.7
F30 A:9MZ404 2.2 0.8 0.7
C25 A:9MZ404 2.3 0.5 0.7
C25 A:0MZ403 2.4 0.1 0.3
F29 A:0MZ403 2.8 0.1 0.3
H24 A:9MZ404 2.8 1.0 0.7
H26 A:0MZ403 2.8 0.4 0.3
C24 A:9MZ404 2.9 0.9 0.7
C26 A:0MZ403 2.9 0.6 0.3
C26 A:9MZ404 3.4 0.6 0.7
C24 A:0MZ403 3.4 0.5 0.3
H26 A:9MZ404 3.6 0.3 0.7
H24 A:0MZ403 3.7 0.5 0.3
O A:LEU101 3.9 0.1 1.0
C21 A:0MZ403 4.2 0.9 0.3
C23 A:9MZ404 4.2 0.3 0.7
C23 A:0MZ403 4.5 0.4 0.3
C21 A:9MZ404 4.6 0.7 0.7
C22 A:0MZ403 4.8 0.2 0.3
C22 A:9MZ404 4.9 1.0 0.7
H23 A:9MZ404 4.9 0.1 0.7

Reference:

E.Carosati, A.Tochowicz, G.Marverti, G.Guaitoli, P.Benedetti, S.Ferrari, R.M.Stroud, J.Finer-Moore, R.Luciani, D.Farina, G.Cruciani, M.P.Costi. Inhibitor of Ovarian Cancer Cells Growth By Virtual Screening: A New Thiazole Derivative Targeting Human Thymidylate Synthase. J.Med.Chem. V. 55 10272 2012.
ISSN: ISSN 0022-2623
PubMed: 23075414
DOI: 10.1021/JM300850V
Page generated: Sun Dec 13 12:01:52 2020

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