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Fluorine in PDB 4yfn: Escherichia Coli Rna Polymerase in Complex with Squaramide Compound 14 (N-[3,4-Dioxo-2-(4-{[4-(Trifluoromethyl)Benzyl]Amino}Piperidin-1-Yl) Cyclobut-1-En-1-Yl]-3,5-Dimethyl-1,2-Oxazole-4-Sulfonamide)

Enzymatic activity of Escherichia Coli Rna Polymerase in Complex with Squaramide Compound 14 (N-[3,4-Dioxo-2-(4-{[4-(Trifluoromethyl)Benzyl]Amino}Piperidin-1-Yl) Cyclobut-1-En-1-Yl]-3,5-Dimethyl-1,2-Oxazole-4-Sulfonamide)

All present enzymatic activity of Escherichia Coli Rna Polymerase in Complex with Squaramide Compound 14 (N-[3,4-Dioxo-2-(4-{[4-(Trifluoromethyl)Benzyl]Amino}Piperidin-1-Yl) Cyclobut-1-En-1-Yl]-3,5-Dimethyl-1,2-Oxazole-4-Sulfonamide):
2.7.7.6;

Protein crystallography data

The structure of Escherichia Coli Rna Polymerase in Complex with Squaramide Compound 14 (N-[3,4-Dioxo-2-(4-{[4-(Trifluoromethyl)Benzyl]Amino}Piperidin-1-Yl) Cyclobut-1-En-1-Yl]-3,5-Dimethyl-1,2-Oxazole-4-Sulfonamide), PDB code: 4yfn was solved by V.Molodtsov, P.R.Fleming, C.J.Eyermann, A.D.Ferguson, M.A.Foulk, D.C.Mckinney, C.E.Masse, E.T.Buurman, K.S.Murakami, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 29.96 / 3.82
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 191.247, 206.569, 312.146, 90.00, 90.00, 90.00
R / Rfree (%) 22.2 / 27

Other elements in 4yfn:

The structure of Escherichia Coli Rna Polymerase in Complex with Squaramide Compound 14 (N-[3,4-Dioxo-2-(4-{[4-(Trifluoromethyl)Benzyl]Amino}Piperidin-1-Yl) Cyclobut-1-En-1-Yl]-3,5-Dimethyl-1,2-Oxazole-4-Sulfonamide) also contains other interesting chemical elements:

Magnesium (Mg) 2 atoms
Zinc (Zn) 4 atoms

Fluorine Binding Sites:

The binding sites of Fluorine atom in the Escherichia Coli Rna Polymerase in Complex with Squaramide Compound 14 (N-[3,4-Dioxo-2-(4-{[4-(Trifluoromethyl)Benzyl]Amino}Piperidin-1-Yl) Cyclobut-1-En-1-Yl]-3,5-Dimethyl-1,2-Oxazole-4-Sulfonamide) (pdb code 4yfn). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 6 binding sites of Fluorine where determined in the Escherichia Coli Rna Polymerase in Complex with Squaramide Compound 14 (N-[3,4-Dioxo-2-(4-{[4-(Trifluoromethyl)Benzyl]Amino}Piperidin-1-Yl) Cyclobut-1-En-1-Yl]-3,5-Dimethyl-1,2-Oxazole-4-Sulfonamide), PDB code: 4yfn:
Jump to Fluorine binding site number: 1; 2; 3; 4; 5; 6;

Fluorine binding site 1 out of 6 in 4yfn

Go back to Fluorine Binding Sites List in 4yfn
Fluorine binding site 1 out of 6 in the Escherichia Coli Rna Polymerase in Complex with Squaramide Compound 14 (N-[3,4-Dioxo-2-(4-{[4-(Trifluoromethyl)Benzyl]Amino}Piperidin-1-Yl) Cyclobut-1-En-1-Yl]-3,5-Dimethyl-1,2-Oxazole-4-Sulfonamide)


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of Escherichia Coli Rna Polymerase in Complex with Squaramide Compound 14 (N-[3,4-Dioxo-2-(4-{[4-(Trifluoromethyl)Benzyl]Amino}Piperidin-1-Yl) Cyclobut-1-En-1-Yl]-3,5-Dimethyl-1,2-Oxazole-4-Sulfonamide) within 5.0Å range:
probe atom residue distance (Å) B Occ
D:F2004

b:0.5
occ:1.00
 F2 D:4C22004 0.0 0.5 1.0
C16 D:4C22004 1.3 0.5 1.0
F D:4C22004 2.1 0.5 1.0
F1 D:4C22004 2.1 0.5 1.0
C15 D:4C22004 2.3 0.5 1.0
C14 D:4C22004 2.7 0.5 1.0
CD1 C:ILE1330 3.0 1.0 1.0
C17 D:4C22004 3.6 0.5 1.0
C13 D:4C22004 4.1 0.5 1.0
CD1 C:ILE1337 4.3 0.0 1.0
CG1 C:ILE1330 4.3 0.3 1.0
CD1 D:LEU1332 4.6 0.6 1.0
CG2 C:ILE1330 4.7 0.2 1.0
C18 D:4C22004 4.7 0.5 1.0
CE1 D:PHE1319 4.9 0.0 1.0
C12 D:4C22004 4.9 0.5 1.0

Fluorine binding site 2 out of 6 in 4yfn

Go back to Fluorine Binding Sites List in 4yfn
Fluorine binding site 2 out of 6 in the Escherichia Coli Rna Polymerase in Complex with Squaramide Compound 14 (N-[3,4-Dioxo-2-(4-{[4-(Trifluoromethyl)Benzyl]Amino}Piperidin-1-Yl) Cyclobut-1-En-1-Yl]-3,5-Dimethyl-1,2-Oxazole-4-Sulfonamide)


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of Escherichia Coli Rna Polymerase in Complex with Squaramide Compound 14 (N-[3,4-Dioxo-2-(4-{[4-(Trifluoromethyl)Benzyl]Amino}Piperidin-1-Yl) Cyclobut-1-En-1-Yl]-3,5-Dimethyl-1,2-Oxazole-4-Sulfonamide) within 5.0Å range:
probe atom residue distance (Å) B Occ
D:F2004

b:0.5
occ:1.00
 F1 D:4C22004 0.0 0.5 1.0
C16 D:4C22004 1.3 0.5 1.0
F D:4C22004 2.1 0.5 1.0
F2 D:4C22004 2.1 0.5 1.0
C15 D:4C22004 2.3 0.5 1.0
C17 D:4C22004 2.9 0.5 1.0
C14 D:4C22004 3.4 0.5 1.0
CE2 C:PHE1323 3.7 0.5 1.0
CG1 D:ILE1320 3.9 0.6 1.0
C18 D:4C22004 4.2 0.5 1.0
CZ C:PHE1323 4.5 0.6 1.0
CD1 C:ILE1330 4.5 1.0 1.0
CG2 D:ILE1320 4.5 0.9 1.0
CD2 C:PHE1323 4.5 0.6 1.0
C13 D:4C22004 4.6 0.5 1.0
CD1 C:ILE1337 4.6 0.0 1.0
CD1 C:LEU1326 4.6 0.9 1.0
CB D:ILE1320 4.7 0.7 1.0
CD1 D:ILE1320 4.7 0.3 1.0
CE1 D:PHE1319 4.8 0.0 1.0
CA D:ILE1320 4.9 0.6 1.0
C12 D:4C22004 4.9 0.5 1.0

Fluorine binding site 3 out of 6 in 4yfn

Go back to Fluorine Binding Sites List in 4yfn
Fluorine binding site 3 out of 6 in the Escherichia Coli Rna Polymerase in Complex with Squaramide Compound 14 (N-[3,4-Dioxo-2-(4-{[4-(Trifluoromethyl)Benzyl]Amino}Piperidin-1-Yl) Cyclobut-1-En-1-Yl]-3,5-Dimethyl-1,2-Oxazole-4-Sulfonamide)


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of Escherichia Coli Rna Polymerase in Complex with Squaramide Compound 14 (N-[3,4-Dioxo-2-(4-{[4-(Trifluoromethyl)Benzyl]Amino}Piperidin-1-Yl) Cyclobut-1-En-1-Yl]-3,5-Dimethyl-1,2-Oxazole-4-Sulfonamide) within 5.0Å range:
probe atom residue distance (Å) B Occ
D:F2004

b:0.5
occ:1.00
 F D:4C22004 0.0 0.5 1.0
C16 D:4C22004 1.3 0.5 1.0
F1 D:4C22004 2.1 0.5 1.0
F2 D:4C22004 2.1 0.5 1.0
C15 D:4C22004 2.3 0.5 1.0
C17 D:4C22004 3.0 0.5 1.0
C14 D:4C22004 3.4 0.5 1.0
CE1 D:PHE1319 3.5 0.0 1.0
CD1 D:PHE1319 3.7 0.5 1.0
CG1 D:ILE1320 4.0 0.6 1.0
CA D:ILE1320 4.1 0.6 1.0
C18 D:4C22004 4.3 0.5 1.0
CB D:ALA1323 4.5 0.9 1.0
CB D:ILE1320 4.5 0.7 1.0
C13 D:4C22004 4.5 0.5 1.0
N D:ILE1320 4.6 0.4 1.0
CD1 D:LEU1332 4.7 0.6 1.0
CZ D:PHE1319 4.7 0.7 1.0
CD1 C:ILE1337 4.8 0.0 1.0
CG2 D:ILE1320 4.8 0.9 1.0
O D:PHE1319 4.9 0.5 1.0
C12 D:4C22004 4.9 0.5 1.0
C D:PHE1319 4.9 0.3 1.0

Fluorine binding site 4 out of 6 in 4yfn

Go back to Fluorine Binding Sites List in 4yfn
Fluorine binding site 4 out of 6 in the Escherichia Coli Rna Polymerase in Complex with Squaramide Compound 14 (N-[3,4-Dioxo-2-(4-{[4-(Trifluoromethyl)Benzyl]Amino}Piperidin-1-Yl) Cyclobut-1-En-1-Yl]-3,5-Dimethyl-1,2-Oxazole-4-Sulfonamide)


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 4 of Escherichia Coli Rna Polymerase in Complex with Squaramide Compound 14 (N-[3,4-Dioxo-2-(4-{[4-(Trifluoromethyl)Benzyl]Amino}Piperidin-1-Yl) Cyclobut-1-En-1-Yl]-3,5-Dimethyl-1,2-Oxazole-4-Sulfonamide) within 5.0Å range:
probe atom residue distance (Å) B Occ
J:F2004

b:0.5
occ:1.00
 F2 J:4C22004 0.0 0.5 1.0
C16 J:4C22004 1.3 0.5 1.0
F J:4C22004 2.1 0.5 1.0
F1 J:4C22004 2.2 0.5 1.0
C15 J:4C22004 2.4 0.5 1.0
C17 J:4C22004 3.0 0.5 1.0
C14 J:4C22004 3.4 0.5 1.0
CE2 I:PHE1323 4.0 0.2 1.0
CD1 I:ILE1337 4.1 0.2 1.0
C18 J:4C22004 4.3 0.5 1.0
CG1 J:ILE1320 4.3 0.9 1.0
CZ I:PHE1323 4.5 0.5 1.0
C13 J:4C22004 4.6 0.5 1.0
CE1 J:PHE1319 4.7 0.2 1.0
CD2 I:PHE1323 4.9 0.9 1.0
CG2 J:ILE1320 4.9 0.5 1.0
C12 J:4C22004 5.0 0.5 1.0

Fluorine binding site 5 out of 6 in 4yfn

Go back to Fluorine Binding Sites List in 4yfn
Fluorine binding site 5 out of 6 in the Escherichia Coli Rna Polymerase in Complex with Squaramide Compound 14 (N-[3,4-Dioxo-2-(4-{[4-(Trifluoromethyl)Benzyl]Amino}Piperidin-1-Yl) Cyclobut-1-En-1-Yl]-3,5-Dimethyl-1,2-Oxazole-4-Sulfonamide)


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 5 of Escherichia Coli Rna Polymerase in Complex with Squaramide Compound 14 (N-[3,4-Dioxo-2-(4-{[4-(Trifluoromethyl)Benzyl]Amino}Piperidin-1-Yl) Cyclobut-1-En-1-Yl]-3,5-Dimethyl-1,2-Oxazole-4-Sulfonamide) within 5.0Å range:
probe atom residue distance (Å) B Occ
J:F2004

b:0.5
occ:1.00
 F1 J:4C22004 0.0 0.5 1.0
C16 J:4C22004 1.3 0.5 1.0
F J:4C22004 2.1 0.5 1.0
F2 J:4C22004 2.2 0.5 1.0
C15 J:4C22004 2.4 0.5 1.0
C17 J:4C22004 3.0 0.5 1.0
C14 J:4C22004 3.4 0.5 1.0
CE1 J:PHE1319 3.4 0.2 1.0
CD1 J:PHE1319 3.5 0.2 1.0
CG1 J:ILE1320 4.0 0.9 1.0
CA J:ILE1320 4.1 0.7 1.0
C18 J:4C22004 4.3 0.5 1.0
CB J:ALA1323 4.5 0.1 1.0
CB J:ILE1320 4.6 0.7 1.0
C13 J:4C22004 4.6 0.5 1.0
N J:ILE1320 4.6 0.1 1.0
O J:PHE1319 4.6 0.4 1.0
CD1 I:ILE1337 4.7 0.2 1.0
CZ J:PHE1319 4.7 0.8 1.0
C J:PHE1319 4.8 0.3 1.0
CG J:PHE1319 4.9 0.6 1.0
CG2 J:ILE1320 4.9 0.5 1.0
C12 J:4C22004 5.0 0.5 1.0

Fluorine binding site 6 out of 6 in 4yfn

Go back to Fluorine Binding Sites List in 4yfn
Fluorine binding site 6 out of 6 in the Escherichia Coli Rna Polymerase in Complex with Squaramide Compound 14 (N-[3,4-Dioxo-2-(4-{[4-(Trifluoromethyl)Benzyl]Amino}Piperidin-1-Yl) Cyclobut-1-En-1-Yl]-3,5-Dimethyl-1,2-Oxazole-4-Sulfonamide)


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 6 of Escherichia Coli Rna Polymerase in Complex with Squaramide Compound 14 (N-[3,4-Dioxo-2-(4-{[4-(Trifluoromethyl)Benzyl]Amino}Piperidin-1-Yl) Cyclobut-1-En-1-Yl]-3,5-Dimethyl-1,2-Oxazole-4-Sulfonamide) within 5.0Å range:
probe atom residue distance (Å) B Occ
J:F2004

b:0.5
occ:1.00
 F J:4C22004 0.0 0.5 1.0
C16 J:4C22004 1.3 0.5 1.0
F1 J:4C22004 2.1 0.5 1.0
F2 J:4C22004 2.1 0.5 1.0
C15 J:4C22004 2.3 0.5 1.0
C14 J:4C22004 2.7 0.5 1.0
C17 J:4C22004 3.6 0.5 1.0
CD1 I:ILE1337 3.9 0.2 1.0
CD1 J:LEU1332 4.0 0.6 1.0
CD1 I:ILE1330 4.0 0.7 1.0
C13 J:4C22004 4.0 0.5 1.0
CE1 J:PHE1319 4.7 0.2 1.0
C18 J:4C22004 4.7 0.5 1.0
CG J:LEU1332 4.8 0.4 1.0
C12 J:4C22004 4.9 0.5 1.0
CG2 I:ILE1330 5.0 0.9 1.0

Reference:

V.Molodtsov, P.R.Fleming, C.J.Eyermann, A.D.Ferguson, M.A.Foulk, D.C.Mckinney, C.E.Masse, E.T.Buurman, K.S.Murakami. X-Ray Crystal Structures of Escherichia Coli Rna Polymerase with Switch Region Binding Inhibitors Enable Rational Design of Squaramides with An Improved Fraction Unbound to Human Plasma Protein To Be Published.
Page generated: Tue Jul 15 01:42:49 2025

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