Cobalt 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:

Fluorine

(F)

3 atoms

The binding sites of Cobalt 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 Cobalt atom.
In total 2 binding sites of Cobalt 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 Cobalt binding site number: 1; 2;

Cobalt binding site 1 out of 2 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 Cobalt with other atoms in the Co 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 A:Co303 b:17.5 occ:1.00 O A:HOH459 2.1 15.9 1.0 O A:HOH446 2.1 18.8 1.0 NE2 B:HIS157 2.1 22.8 1.0 O B:HOH444 2.1 14.8 1.0 NE2 A:HIS38 2.1 18.1 1.0 O B:HOH482 2.2 23.3 1.0 CD2 B:HIS157 3.0 24.7 1.0 CD2 A:HIS38 3.1 18.0 1.0 CE1 B:HIS157 3.1 26.8 1.0 CE1 A:HIS38 3.1 19.0 1.0 O A:ILE34 3.8 14.7 1.0 OE1 A:GLU90 3.9 19.3 1.0 OG1 B:THR108 4.1 24.4 1.0 O A:MET36 4.1 14.8 1.0 OE2 A:GLU90 4.1 28.5 1.0 ND1 B:HIS157 4.2 27.5 1.0 CG B:HIS157 4.2 25.0 1.0 ND1 A:HIS38 4.2 20.1 1.0 CG A:HIS38 4.2 17.5 1.0 CD A:GLU90 4.4 23.1 1.0 O A:GLU33 4.5 18.7 1.0 O A:HOH477 4.6 23.3 1.0 O B:ARG158 4.7 37.0 1.0 C A:ILE34 4.7 17.2 1.0

Cobalt binding site 2 out of 2 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 Cobalt with other atoms in the Co 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:Co304 b:20.6 occ:1.00 O A:HOH448 2.0 20.2 1.0 O A:HOH430 2.1 19.6 1.0 NE2 B:HIS38 2.1 16.7 1.0 O B:HOH407 2.1 16.5 1.0 O B:HOH435 2.2 17.2 1.0 O B:HOH408 2.4 22.5 1.0 CD2 B:HIS38 3.0 17.6 1.0 CE1 B:HIS38 3.1 16.3 1.0 O A:HOH486 3.8 33.8 1.0 OE1 B:GLU90 3.8 18.1 1.0 O B:ILE34 3.8 15.4 1.0 O B:HOH420 4.0 19.8 1.0 OE2 B:GLU90 4.0 19.5 1.0 O B:MET36 4.1 17.0 1.0 CE1 A:HIS157 4.2 30.0 1.0 CG B:HIS38 4.2 16.3 1.0 ND1 B:HIS38 4.2 18.4 1.0 CD B:GLU90 4.2 21.2 1.0 O A:SER159 4.3 24.1 1.0 NE2 A:HIS157 4.4 24.9 1.0 O A:ARG158 4.5 20.3 1.0 O B:GLU33 4.5 18.0 1.0 CA A:SER159 4.5 20.4 1.0 O B:HOH428 4.5 24.9 1.0 CG2 A:THR108 4.7 20.1 1.0 O B:HOH495 4.7 32.2 1.0 CB A:THR108 4.7 19.7 1.0 C B:ILE34 4.7 16.2 1.0 OG1 A:THR108 4.8 19.4 1.0 C A:SER159 4.8 22.9 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.