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Fluorine in PDB 6lkm: Crystal Structure of Ribonucleotide Reductase R1 Subunit, RRM1 in Complex with 5-Chloro-N-((1S,2R)-2-(6-Fluoro-2,3-Dimethylphenyl)-1- (5-Oxo-4,5-Dihydro-1,3,4-Oxadiazol-2-Yl)Propyl)-4-Methyl-3,4-Dihydro- 2H-Benzo[B][1,4]Oxazine-8-Sulfonamide

Enzymatic activity of Crystal Structure of Ribonucleotide Reductase R1 Subunit, RRM1 in Complex with 5-Chloro-N-((1S,2R)-2-(6-Fluoro-2,3-Dimethylphenyl)-1- (5-Oxo-4,5-Dihydro-1,3,4-Oxadiazol-2-Yl)Propyl)-4-Methyl-3,4-Dihydro- 2H-Benzo[B][1,4]Oxazine-8-Sulfonamide

All present enzymatic activity of Crystal Structure of Ribonucleotide Reductase R1 Subunit, RRM1 in Complex with 5-Chloro-N-((1S,2R)-2-(6-Fluoro-2,3-Dimethylphenyl)-1- (5-Oxo-4,5-Dihydro-1,3,4-Oxadiazol-2-Yl)Propyl)-4-Methyl-3,4-Dihydro- 2H-Benzo[B][1,4]Oxazine-8-Sulfonamide:
1.17.4.1;

Protein crystallography data

The structure of Crystal Structure of Ribonucleotide Reductase R1 Subunit, RRM1 in Complex with 5-Chloro-N-((1S,2R)-2-(6-Fluoro-2,3-Dimethylphenyl)-1- (5-Oxo-4,5-Dihydro-1,3,4-Oxadiazol-2-Yl)Propyl)-4-Methyl-3,4-Dihydro- 2H-Benzo[B][1,4]Oxazine-8-Sulfonamide, PDB code: 6lkm was solved by S.Miyahara, K.T.Chong, T.Suzuki, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 110.62 / 2.55
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 227.830, 66.920, 110.000, 90.00, 103.82, 90.00
R / Rfree (%) 21 / 27.7

Other elements in 6lkm:

The structure of Crystal Structure of Ribonucleotide Reductase R1 Subunit, RRM1 in Complex with 5-Chloro-N-((1S,2R)-2-(6-Fluoro-2,3-Dimethylphenyl)-1- (5-Oxo-4,5-Dihydro-1,3,4-Oxadiazol-2-Yl)Propyl)-4-Methyl-3,4-Dihydro- 2H-Benzo[B][1,4]Oxazine-8-Sulfonamide also contains other interesting chemical elements:

Magnesium (Mg) 2 atoms
Chlorine (Cl) 2 atoms

Fluorine Binding Sites:

The binding sites of Fluorine atom in the Crystal Structure of Ribonucleotide Reductase R1 Subunit, RRM1 in Complex with 5-Chloro-N-((1S,2R)-2-(6-Fluoro-2,3-Dimethylphenyl)-1- (5-Oxo-4,5-Dihydro-1,3,4-Oxadiazol-2-Yl)Propyl)-4-Methyl-3,4-Dihydro- 2H-Benzo[B][1,4]Oxazine-8-Sulfonamide (pdb code 6lkm). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 2 binding sites of Fluorine where determined in the Crystal Structure of Ribonucleotide Reductase R1 Subunit, RRM1 in Complex with 5-Chloro-N-((1S,2R)-2-(6-Fluoro-2,3-Dimethylphenyl)-1- (5-Oxo-4,5-Dihydro-1,3,4-Oxadiazol-2-Yl)Propyl)-4-Methyl-3,4-Dihydro- 2H-Benzo[B][1,4]Oxazine-8-Sulfonamide, PDB code: 6lkm:
Jump to Fluorine binding site number: 1; 2;

Fluorine binding site 1 out of 2 in 6lkm

Go back to Fluorine Binding Sites List in 6lkm
Fluorine binding site 1 out of 2 in the Crystal Structure of Ribonucleotide Reductase R1 Subunit, RRM1 in Complex with 5-Chloro-N-((1S,2R)-2-(6-Fluoro-2,3-Dimethylphenyl)-1- (5-Oxo-4,5-Dihydro-1,3,4-Oxadiazol-2-Yl)Propyl)-4-Methyl-3,4-Dihydro- 2H-Benzo[B][1,4]Oxazine-8-Sulfonamide


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of Crystal Structure of Ribonucleotide Reductase R1 Subunit, RRM1 in Complex with 5-Chloro-N-((1S,2R)-2-(6-Fluoro-2,3-Dimethylphenyl)-1- (5-Oxo-4,5-Dihydro-1,3,4-Oxadiazol-2-Yl)Propyl)-4-Methyl-3,4-Dihydro- 2H-Benzo[B][1,4]Oxazine-8-Sulfonamide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F803

b:50.3
occ:1.00
 F9 A:EJ6803 0.0 50.3 1.0
C3 A:EJ6803 1.3 53.0 1.0
C2 A:EJ6803 2.4 51.1 1.0
C4 A:EJ6803 2.4 57.6 1.0
C10 A:EJ6803 2.9 59.1 1.0
C11 A:EJ6803 3.0 63.6 1.0
CB A:GLN688 3.0 46.0 1.0
C12 A:EJ6803 3.1 59.5 1.0
C14 A:EJ6803 3.4 68.2 1.0
N18 A:EJ6803 3.5 66.8 1.0
C1 A:EJ6803 3.6 52.9 1.0
CB A:MET723 3.7 47.3 1.0
CG A:MET723 3.7 50.7 1.0
C5 A:EJ6803 3.8 58.7 1.0
CG A:GLN688 3.9 46.9 1.0
CD1 A:ILE712 4.1 44.1 1.0
CA A:GLN688 4.1 45.6 1.0
C A:GLN688 4.2 45.2 1.0
C6 A:EJ6803 4.2 56.0 1.0
N13 A:EJ6803 4.2 67.8 1.0
N A:LYS689 4.2 47.0 1.0
CG1 A:ILE712 4.5 45.9 1.0
CA A:MET723 4.5 46.6 1.0
O15 A:EJ6803 4.5 69.2 1.0
N A:GLN688 4.7 42.9 1.0
N17 A:EJ6803 4.7 64.2 1.0
O21 A:EJ6803 4.8 72.2 1.0
O A:GLN688 4.8 50.5 1.0

Fluorine binding site 2 out of 2 in 6lkm

Go back to Fluorine Binding Sites List in 6lkm
Fluorine binding site 2 out of 2 in the Crystal Structure of Ribonucleotide Reductase R1 Subunit, RRM1 in Complex with 5-Chloro-N-((1S,2R)-2-(6-Fluoro-2,3-Dimethylphenyl)-1- (5-Oxo-4,5-Dihydro-1,3,4-Oxadiazol-2-Yl)Propyl)-4-Methyl-3,4-Dihydro- 2H-Benzo[B][1,4]Oxazine-8-Sulfonamide


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of Crystal Structure of Ribonucleotide Reductase R1 Subunit, RRM1 in Complex with 5-Chloro-N-((1S,2R)-2-(6-Fluoro-2,3-Dimethylphenyl)-1- (5-Oxo-4,5-Dihydro-1,3,4-Oxadiazol-2-Yl)Propyl)-4-Methyl-3,4-Dihydro- 2H-Benzo[B][1,4]Oxazine-8-Sulfonamide within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F803

b:38.8
occ:1.00
 F9 B:EJ6803 0.0 38.8 1.0
C3 B:EJ6803 1.3 38.4 1.0
C2 B:EJ6803 2.4 34.3 1.0
C4 B:EJ6803 2.5 42.0 1.0
C10 B:EJ6803 3.0 46.8 1.0
C11 B:EJ6803 3.1 49.9 1.0
CB B:MET723 3.2 36.2 1.0
C12 B:EJ6803 3.3 47.6 1.0
CB B:GLN688 3.3 39.5 1.0
C14 B:EJ6803 3.4 49.2 1.0
N18 B:EJ6803 3.6 49.5 1.0
C1 B:EJ6803 3.6 35.3 1.0
C5 B:EJ6803 3.8 42.8 1.0
CG B:MET723 4.1 39.8 1.0
C B:GLN688 4.1 35.5 1.0
N B:LYS689 4.1 35.7 1.0
CA B:GLN688 4.2 38.5 1.0
C6 B:EJ6803 4.2 39.4 1.0
CA B:MET723 4.3 36.3 1.0
O15 B:EJ6803 4.3 51.3 1.0
CD1 B:ILE712 4.3 41.5 1.0
CG B:GLN688 4.4 40.8 1.0
N13 B:EJ6803 4.4 55.9 1.0
O B:GLN688 4.5 39.1 1.0
N17 B:EJ6803 4.7 48.9 1.0
CG1 B:ILE712 4.8 42.4 1.0
CA B:LYS689 4.8 37.4 1.0
N B:GLN688 4.8 37.9 1.0
CD2 B:LEU692 4.8 42.1 1.0
N B:MET723 4.9 33.9 1.0
O21 B:EJ6803 4.9 50.5 1.0
C16 B:EJ6803 4.9 51.2 1.0
SD B:MET723 5.0 39.5 1.0

Reference:

S.Miyahara, S.Hara, K.T.Chong, T.Suzuki, Y.Ogino, T.Hoshino, S.Tsukioka, W.Yano, M.Suzuki, Y.Otsu, T.Yonekura, S.Ito, M.Terasaka, T.Suzuki, A.Hashimoto. TAS1553, A Novel Small Molecule Ribonucleotide Reductase (Rnr) Subunit Interaction Inhibitor, Displays Remarkable Anti-Tumor Activity To Be Published.
Page generated: Tue Jul 15 12:56:35 2025

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