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Fluorine in PDB 4qjc: Human Dihydrofolate Reductase Ternary Complex with Nadph and Inhibitor 26 (N~6~-Methyl-N~6~-(3,4,5-Trifluorophenyl)Pyrido[2,3-D]Pyrimidine- 2,4,6-Triamine)

Enzymatic activity of Human Dihydrofolate Reductase Ternary Complex with Nadph and Inhibitor 26 (N~6~-Methyl-N~6~-(3,4,5-Trifluorophenyl)Pyrido[2,3-D]Pyrimidine- 2,4,6-Triamine)

All present enzymatic activity of Human Dihydrofolate Reductase Ternary Complex with Nadph and Inhibitor 26 (N~6~-Methyl-N~6~-(3,4,5-Trifluorophenyl)Pyrido[2,3-D]Pyrimidine- 2,4,6-Triamine):
1.5.1.3;

Protein crystallography data

The structure of Human Dihydrofolate Reductase Ternary Complex with Nadph and Inhibitor 26 (N~6~-Methyl-N~6~-(3,4,5-Trifluorophenyl)Pyrido[2,3-D]Pyrimidine- 2,4,6-Triamine), PDB code: 4qjc was solved by V.Cody, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 34.37 / 1.62
Space group H 3
Cell size a, b, c (Å), α, β, γ (°) 84.486, 84.486, 77.872, 90.00, 90.00, 120.00
R / Rfree (%) 18.3 / 21.8

Fluorine Binding Sites:

The binding sites of Fluorine atom in the Human Dihydrofolate Reductase Ternary Complex with Nadph and Inhibitor 26 (N~6~-Methyl-N~6~-(3,4,5-Trifluorophenyl)Pyrido[2,3-D]Pyrimidine- 2,4,6-Triamine) (pdb code 4qjc). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 3 binding sites of Fluorine where determined in the Human Dihydrofolate Reductase Ternary Complex with Nadph and Inhibitor 26 (N~6~-Methyl-N~6~-(3,4,5-Trifluorophenyl)Pyrido[2,3-D]Pyrimidine- 2,4,6-Triamine), PDB code: 4qjc:
Jump to Fluorine binding site number: 1; 2; 3;

Fluorine binding site 1 out of 3 in 4qjc

Go back to Fluorine Binding Sites List in 4qjc
Fluorine binding site 1 out of 3 in the Human Dihydrofolate Reductase Ternary Complex with Nadph and Inhibitor 26 (N~6~-Methyl-N~6~-(3,4,5-Trifluorophenyl)Pyrido[2,3-D]Pyrimidine- 2,4,6-Triamine)


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of Human Dihydrofolate Reductase Ternary Complex with Nadph and Inhibitor 26 (N~6~-Methyl-N~6~-(3,4,5-Trifluorophenyl)Pyrido[2,3-D]Pyrimidine- 2,4,6-Triamine) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F202

b:39.0
occ:1.00
 F1 A:IXE202 0.0 39.0 1.0
C11 A:IXE202 1.2 38.8 1.0
C12 A:IXE202 2.2 44.8 1.0
C10 A:IXE202 2.3 36.0 1.0
F2 A:IXE202 2.7 50.0 1.0
O A:SER59 3.3 20.6 1.0
C13 A:IXE202 3.5 44.0 1.0
OD1 A:ASP21 3.5 39.9 1.0
CA A:ASP21 3.5 18.9 1.0
C9 A:IXE202 3.6 34.7 1.0
O A:GLY20 3.7 24.2 1.0
N A:LEU22 3.7 20.0 1.0
C A:ASP21 3.9 21.1 1.0
O2D A:NDP201 3.9 35.2 1.0
CB A:SER59 4.0 17.9 1.0
OG A:SER59 4.0 22.6 1.0
C14 A:IXE202 4.0 38.1 1.0
C A:SER59 4.1 19.7 1.0
CG A:LEU22 4.2 22.6 1.0
CG A:ASP21 4.2 35.1 1.0
CD2 A:LEU22 4.3 24.0 1.0
C A:GLY20 4.4 21.3 1.0
N A:ASP21 4.4 18.8 1.0
CB A:ASP21 4.5 25.5 1.0
CA A:SER59 4.5 15.8 1.0
F3 A:IXE202 4.6 43.3 1.0
N1 A:IXE202 4.7 36.4 1.0
O A:ASP21 4.7 22.1 1.0
C2D A:NDP201 4.7 29.4 1.0
CA A:LEU22 4.8 22.2 1.0
CB A:LEU22 5.0 22.0 1.0

Fluorine binding site 2 out of 3 in 4qjc

Go back to Fluorine Binding Sites List in 4qjc
Fluorine binding site 2 out of 3 in the Human Dihydrofolate Reductase Ternary Complex with Nadph and Inhibitor 26 (N~6~-Methyl-N~6~-(3,4,5-Trifluorophenyl)Pyrido[2,3-D]Pyrimidine- 2,4,6-Triamine)


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of Human Dihydrofolate Reductase Ternary Complex with Nadph and Inhibitor 26 (N~6~-Methyl-N~6~-(3,4,5-Trifluorophenyl)Pyrido[2,3-D]Pyrimidine- 2,4,6-Triamine) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F202

b:50.0
occ:1.00
 F2 A:IXE202 0.0 50.0 1.0
C12 A:IXE202 1.6 44.8 1.0
C11 A:IXE202 2.6 38.8 1.0
C13 A:IXE202 2.7 44.0 1.0
F1 A:IXE202 2.7 39.0 1.0
F3 A:IXE202 2.9 43.3 1.0
OD1 A:ASP21 3.4 39.9 1.0
O A:SER59 3.4 20.6 1.0
C10 A:IXE202 3.9 36.0 1.0
C14 A:IXE202 4.0 38.1 1.0
CD A:PRO61 4.0 32.4 1.0
CG A:PRO61 4.3 34.6 1.0
CG A:ASP21 4.3 35.1 1.0
C9 A:IXE202 4.5 34.7 1.0
C A:SER59 4.7 19.7 1.0
OD2 A:ASP21 4.8 42.6 1.0

Fluorine binding site 3 out of 3 in 4qjc

Go back to Fluorine Binding Sites List in 4qjc
Fluorine binding site 3 out of 3 in the Human Dihydrofolate Reductase Ternary Complex with Nadph and Inhibitor 26 (N~6~-Methyl-N~6~-(3,4,5-Trifluorophenyl)Pyrido[2,3-D]Pyrimidine- 2,4,6-Triamine)


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of Human Dihydrofolate Reductase Ternary Complex with Nadph and Inhibitor 26 (N~6~-Methyl-N~6~-(3,4,5-Trifluorophenyl)Pyrido[2,3-D]Pyrimidine- 2,4,6-Triamine) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F202

b:43.3
occ:1.00
 F3 A:IXE202 0.0 43.3 1.0
C13 A:IXE202 1.5 44.0 1.0
C12 A:IXE202 2.4 44.8 1.0
C14 A:IXE202 2.6 38.1 1.0
F2 A:IXE202 2.9 50.0 1.0
CD A:PRO61 3.5 32.4 1.0
C11 A:IXE202 3.7 38.8 1.0
C9 A:IXE202 3.8 34.7 1.0
CG A:PRO61 3.9 34.6 1.0
C10 A:IXE202 4.3 36.0 1.0
CE1 A:PHE31 4.5 36.1 1.0
CZ A:PHE31 4.6 33.5 1.0
F1 A:IXE202 4.6 39.0 1.0
O A:SER59 4.8 20.6 1.0
CD1 A:PHE31 4.8 33.0 1.0
N A:PRO61 4.9 29.0 1.0

Reference:

V.Cody, J.Pace, O.A.Namjoshi, A.Gangjee. Structure-Activity Correlations For Three Pyrido[2,3-D]Pyrimidine Antifolates Binding to Human and Pneumocystis Carinii Dihydrofolate Reductase. Acta Crystallogr F Struct V. 71 799 2015BIOL Commun.
ISSN: ESSN 1744-3091
PubMed: 26057816
DOI: 10.1107/S2053230X15008468
Page generated: Thu Aug 1 05:14:04 2024

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