Fluorine in PDB 8cq9: Mycobacterium Tuberculosis Dihydrofolate Reductase in Complex with 5- (Cyclopropylethynyl)-6-(4-(Trifluoromethyl)Phenyl)Pyrimidine-2,4- Diamine

The structure of Mycobacterium Tuberculosis Dihydrofolate Reductase in Complex with 5- (Cyclopropylethynyl)-6-(4-(Trifluoromethyl)Phenyl)Pyrimidine-2,4- Diamine, PDB code: 8cq9 was solved by T.J.Kirkman, M.V.B.Dias, A.G.Coyne, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	36.22 / 1.75
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	61.658, 71.068, 72.43, 90, 90, 90
R / Rfree (%)	19.9 / 22.8

The structure of Mycobacterium Tuberculosis Dihydrofolate Reductase in Complex with 5- (Cyclopropylethynyl)-6-(4-(Trifluoromethyl)Phenyl)Pyrimidine-2,4- Diamine also contains other interesting chemical elements:

Cobalt

(Co)

2 atoms

The binding sites of Fluorine atom in the Mycobacterium Tuberculosis Dihydrofolate Reductase in Complex with 5- (Cyclopropylethynyl)-6-(4-(Trifluoromethyl)Phenyl)Pyrimidine-2,4- Diamine (pdb code 8cq9). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 3 binding sites of Fluorine where determined in the Mycobacterium Tuberculosis Dihydrofolate Reductase in Complex with 5- (Cyclopropylethynyl)-6-(4-(Trifluoromethyl)Phenyl)Pyrimidine-2,4- Diamine, PDB code: 8cq9:
Jump to Fluorine binding site number: 1; 2; 3;

Fluorine binding site 1 out of 3 in the Mycobacterium Tuberculosis Dihydrofolate Reductase in Complex with 5- (Cyclopropylethynyl)-6-(4-(Trifluoromethyl)Phenyl)Pyrimidine-2,4- Diamine


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of Mycobacterium Tuberculosis Dihydrofolate Reductase in Complex with 5- (Cyclopropylethynyl)-6-(4-(Trifluoromethyl)Phenyl)Pyrimidine-2,4- Diamine within 5.0Å range: probe atom residue distance (Å) B Occ B:F301 b:40.0 occ:1.00 F18 B:VFU301 0.0 40.0 1.0 C17 B:VFU301 1.4 35.1 1.0 F19 B:VFU301 2.3 41.2 1.0 F20 B:VFU301 2.3 38.8 1.0 C16 B:VFU301 2.3 30.3 1.0 C21 B:VFU301 2.7 30.1 1.0 C5 B:MES302 3.2 34.6 1.0 C15 B:VFU301 3.6 30.8 1.0 OE1 B:GLN28 3.7 30.8 1.0 C2 B:MES302 3.8 37.9 1.0 C6 B:MES302 3.8 36.5 1.0 CD B:GLN28 3.9 34.6 1.0 N4 B:MES302 4.0 36.5 1.0 C22 B:VFU301 4.1 27.5 1.0 O1 B:MES302 4.1 38.8 1.0 O B:HOH499 4.1 39.2 1.0 NE2 B:GLN28 4.3 34.8 1.0 C3 B:MES302 4.4 34.2 1.0 CG B:GLN28 4.5 32.4 1.0 C7 B:MES302 4.6 28.7 1.0 C14 B:VFU301 4.7 26.0 1.0 C13 B:VFU301 4.9 22.2 1.0 O B:HOH449 4.9 26.7 1.0 O B:HOH514 5.0 44.7 1.0 CB B:GLN28 5.0 25.5 1.0

Fluorine binding site 2 out of 3 in the Mycobacterium Tuberculosis Dihydrofolate Reductase in Complex with 5- (Cyclopropylethynyl)-6-(4-(Trifluoromethyl)Phenyl)Pyrimidine-2,4- Diamine


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of Mycobacterium Tuberculosis Dihydrofolate Reductase in Complex with 5- (Cyclopropylethynyl)-6-(4-(Trifluoromethyl)Phenyl)Pyrimidine-2,4- Diamine within 5.0Å range: probe atom residue distance (Å) B Occ B:F301 b:41.2 occ:1.00 F19 B:VFU301 0.0 41.2 1.0 C17 B:VFU301 1.4 35.1 1.0 F20 B:VFU301 2.2 38.8 1.0 F18 B:VFU301 2.3 40.0 1.0 C16 B:VFU301 2.4 30.3 1.0 C15 B:VFU301 2.8 30.8 1.0 O B:HOH449 3.0 26.7 1.0 C21 B:VFU301 3.6 30.1 1.0 O B:HOH462 3.7 26.2 1.0 O B:HOH508 3.9 29.8 1.0 O B:HOH475 4.1 25.4 1.0 C14 B:VFU301 4.1 26.0 1.0 NE B:ARG23 4.3 26.1 1.0 O B:HOH470 4.4 33.5 1.0 O B:HOH499 4.4 39.2 1.0 CD B:ARG23 4.4 26.7 1.0 C22 B:VFU301 4.7 27.5 1.0 CD1 B:ILE20 4.8 21.5 1.0 C13 B:VFU301 4.9 22.2 1.0 C5 B:MES302 5.0 34.6 1.0

Fluorine binding site 3 out of 3 in the Mycobacterium Tuberculosis Dihydrofolate Reductase in Complex with 5- (Cyclopropylethynyl)-6-(4-(Trifluoromethyl)Phenyl)Pyrimidine-2,4- Diamine


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of Mycobacterium Tuberculosis Dihydrofolate Reductase in Complex with 5- (Cyclopropylethynyl)-6-(4-(Trifluoromethyl)Phenyl)Pyrimidine-2,4- Diamine within 5.0Å range: probe atom residue distance (Å) B Occ B:F301 b:38.8 occ:1.00 F20 B:VFU301 0.0 38.8 1.0 C17 B:VFU301 1.4 35.1 1.0 F19 B:VFU301 2.2 41.2 1.0 F18 B:VFU301 2.3 40.0 1.0 C16 B:VFU301 2.4 30.3 1.0 O B:HOH475 3.0 25.4 1.0 C15 B:VFU301 3.2 30.8 1.0 OE1 B:GLN28 3.2 30.8 1.0 C21 B:VFU301 3.3 30.1 1.0 O B:HOH449 3.5 26.7 1.0 O B:HOH499 3.7 39.2 1.0 CD B:GLN28 3.9 34.6 1.0 CD B:ARG23 4.2 26.7 1.0 CB B:GLN28 4.3 25.5 1.0 C14 B:VFU301 4.4 26.0 1.0 CG B:GLN28 4.4 32.4 1.0 C22 B:VFU301 4.5 27.5 1.0 NE B:ARG23 4.7 26.1 1.0 NE2 B:GLN28 4.8 34.8 1.0 C13 B:VFU301 5.0 22.2 1.0

T.J.Kirkman, M.V.B.Dias, A.G.Coyne. Expansion of A Series of Pyrimidine Derivatives Utilising Fragment-Based Merging Leads to Increased Affinity to Mycobacterium Tuberculosis Dihydrofolate Reductase (Unpublished Currently) To Be Published.