Chlorine in PDB 6pf8: Crystal Structure of Ts-Dhfr From Cryptosporidium Hominis in Complex with Nadph, Fdump and 2-(4-((2-Amino-4-Oxo-4,7-Dihydro-3H-Pyrrolo[2, 3-D]Pyrimidin-5-Yl)Methyl)Benzamido)-4-Chlorobenzoic Acid

The structure of Crystal Structure of Ts-Dhfr From Cryptosporidium Hominis in Complex with Nadph, Fdump and 2-(4-((2-Amino-4-Oxo-4,7-Dihydro-3H-Pyrrolo[2, 3-D]Pyrimidin-5-Yl)Methyl)Benzamido)-4-Chlorobenzoic Acid, PDB code: 6pf8 was solved by D.J.Czyzyk, M.Valhondo, W.L.Jorgensen, K.S.Anderson, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	47.88 / 2.53
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	214.777, 117.537, 222.817, 90.00, 95.65, 90.00
R / Rfree (%)	20.2 / 22.6

The structure of Crystal Structure of Ts-Dhfr From Cryptosporidium Hominis in Complex with Nadph, Fdump and 2-(4-((2-Amino-4-Oxo-4,7-Dihydro-3H-Pyrrolo[2, 3-D]Pyrimidin-5-Yl)Methyl)Benzamido)-4-Chlorobenzoic Acid also contains other interesting chemical elements:

Fluorine

(F)

5 atoms

The binding sites of Chlorine atom in the Crystal Structure of Ts-Dhfr From Cryptosporidium Hominis in Complex with Nadph, Fdump and 2-(4-((2-Amino-4-Oxo-4,7-Dihydro-3H-Pyrrolo[2, 3-D]Pyrimidin-5-Yl)Methyl)Benzamido)-4-Chlorobenzoic Acid (pdb code 6pf8). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 5 binding sites of Chlorine where determined in the Crystal Structure of Ts-Dhfr From Cryptosporidium Hominis in Complex with Nadph, Fdump and 2-(4-((2-Amino-4-Oxo-4,7-Dihydro-3H-Pyrrolo[2, 3-D]Pyrimidin-5-Yl)Methyl)Benzamido)-4-Chlorobenzoic Acid, PDB code: 6pf8:
Jump to Chlorine binding site number: 1; 2; 3; 4; 5;

Chlorine binding site 1 out of 5 in the Crystal Structure of Ts-Dhfr From Cryptosporidium Hominis in Complex with Nadph, Fdump and 2-(4-((2-Amino-4-Oxo-4,7-Dihydro-3H-Pyrrolo[2, 3-D]Pyrimidin-5-Yl)Methyl)Benzamido)-4-Chlorobenzoic Acid


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of Crystal Structure of Ts-Dhfr From Cryptosporidium Hominis in Complex with Nadph, Fdump and 2-(4-((2-Amino-4-Oxo-4,7-Dihydro-3H-Pyrrolo[2, 3-D]Pyrimidin-5-Yl)Methyl)Benzamido)-4-Chlorobenzoic Acid within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl603 b:97.0 occ:1.00 CL1 A:OE7603 0.0 97.0 1.0 C17 A:OE7603 1.7 69.7 1.0 C16 A:OE7603 2.7 44.1 1.0 C18 A:OE7603 2.7 97.1 1.0 O A:ILE515 3.1 51.5 1.0 NZ A:LYS284 3.8 39.1 1.0 CD A:LYS284 4.0 47.5 1.0 C19 A:OE7603 4.0 90.1 1.0 C15 A:OE7603 4.0 58.8 1.0 O A:HOH780 4.1 37.5 1.0 CE A:LYS284 4.1 35.9 1.0 CD2 A:LEU429 4.1 52.8 1.0 CE A:MET517 4.2 51.2 1.0 C A:ILE515 4.3 45.0 1.0 C20 A:OE7603 4.6 75.0 1.0 CG A:LYS284 4.8 44.5 1.0 CG2 A:THR514 4.9 45.1 1.0 N A:MET517 4.9 35.3 1.0 N A:ILE515 4.9 48.1 1.0 O A:LYS285 5.0 47.7 1.0

Chlorine binding site 2 out of 5 in the Crystal Structure of Ts-Dhfr From Cryptosporidium Hominis in Complex with Nadph, Fdump and 2-(4-((2-Amino-4-Oxo-4,7-Dihydro-3H-Pyrrolo[2, 3-D]Pyrimidin-5-Yl)Methyl)Benzamido)-4-Chlorobenzoic Acid


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of Crystal Structure of Ts-Dhfr From Cryptosporidium Hominis in Complex with Nadph, Fdump and 2-(4-((2-Amino-4-Oxo-4,7-Dihydro-3H-Pyrrolo[2, 3-D]Pyrimidin-5-Yl)Methyl)Benzamido)-4-Chlorobenzoic Acid within 5.0Å range: probe atom residue distance (Å) B Occ B:Cl603 b:93.4 occ:1.00 CL1 B:OE7603 0.0 93.4 1.0 C17 B:OE7603 1.7 59.8 1.0 C16 B:OE7603 2.7 44.2 1.0 C18 B:OE7603 2.7 83.8 1.0 O B:HOH755 3.1 34.9 1.0 O B:ILE515 3.1 48.2 1.0 O B:HOH772 3.4 41.7 1.0 O B:HOH764 3.7 48.9 1.0 NZ B:LYS284 3.8 37.4 1.0 C19 B:OE7603 4.0 81.1 1.0 C15 B:OE7603 4.0 58.2 1.0 CD B:LYS284 4.1 44.2 1.0 CD2 B:LEU429 4.2 37.3 1.0 CE B:LYS284 4.2 33.9 1.0 O B:HOH808 4.2 35.9 1.0 C B:ILE515 4.3 36.9 1.0 CE B:MET517 4.4 38.9 1.0 C20 B:OE7603 4.6 59.3 1.0 N B:MET517 4.9 31.7 1.0 CG2 B:THR514 4.9 46.8 1.0 N B:ILE515 4.9 35.8 1.0 CG B:LYS284 5.0 44.0 1.0 O B:LYS285 5.0 36.5 1.0

Chlorine binding site 3 out of 5 in the Crystal Structure of Ts-Dhfr From Cryptosporidium Hominis in Complex with Nadph, Fdump and 2-(4-((2-Amino-4-Oxo-4,7-Dihydro-3H-Pyrrolo[2, 3-D]Pyrimidin-5-Yl)Methyl)Benzamido)-4-Chlorobenzoic Acid


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 3 of Crystal Structure of Ts-Dhfr From Cryptosporidium Hominis in Complex with Nadph, Fdump and 2-(4-((2-Amino-4-Oxo-4,7-Dihydro-3H-Pyrrolo[2, 3-D]Pyrimidin-5-Yl)Methyl)Benzamido)-4-Chlorobenzoic Acid within 5.0Å range: probe atom residue distance (Å) B Occ C:Cl603 b:98.8 occ:1.00 CL1 C:OE7603 0.0 98.8 1.0 C17 C:OE7603 1.7 75.4 1.0 C16 C:OE7603 2.7 59.9 1.0 C18 C:OE7603 2.7 84.0 1.0 O C:HOH741 3.0 53.7 1.0 O C:ILE515 3.1 54.9 1.0 NZ C:LYS284 3.6 51.5 1.0 CD C:LYS284 3.7 58.6 1.0 O C:HOH753 3.8 48.5 1.0 CE C:LYS284 3.9 51.1 1.0 CE C:MET517 3.9 60.0 1.0 O C:HOH764 4.0 49.3 1.0 C19 C:OE7603 4.0 78.2 1.0 C15 C:OE7603 4.0 66.6 1.0 O C:HOH788 4.1 54.8 1.0 C C:ILE515 4.3 57.7 1.0 CD2 C:LEU429 4.3 55.0 1.0 C20 C:OE7603 4.6 69.0 1.0 CG C:LYS284 4.6 52.2 1.0 N C:ILE515 4.9 55.9 1.0 O C:LYS285 4.9 45.6 1.0 N C:MET517 4.9 50.4 1.0

Chlorine binding site 4 out of 5 in the Crystal Structure of Ts-Dhfr From Cryptosporidium Hominis in Complex with Nadph, Fdump and 2-(4-((2-Amino-4-Oxo-4,7-Dihydro-3H-Pyrrolo[2, 3-D]Pyrimidin-5-Yl)Methyl)Benzamido)-4-Chlorobenzoic Acid


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 4 of Crystal Structure of Ts-Dhfr From Cryptosporidium Hominis in Complex with Nadph, Fdump and 2-(4-((2-Amino-4-Oxo-4,7-Dihydro-3H-Pyrrolo[2, 3-D]Pyrimidin-5-Yl)Methyl)Benzamido)-4-Chlorobenzoic Acid within 5.0Å range: probe atom residue distance (Å) B Occ D:Cl603 b:93.3 occ:1.00 CL1 D:OE7603 0.0 93.3 1.0 C17 D:OE7603 1.7 57.8 1.0 C16 D:OE7603 2.7 48.3 1.0 C18 D:OE7603 2.7 79.2 1.0 O D:ILE515 3.2 42.2 1.0 NZ D:LYS284 3.5 41.2 1.0 O D:HOH790 3.7 42.5 1.0 CD D:LYS284 3.9 59.6 1.0 CE D:LYS284 4.0 47.5 1.0 O D:HOH762 4.0 43.2 1.0 CD2 D:LEU429 4.0 43.7 1.0 C19 D:OE7603 4.0 73.2 1.0 C15 D:OE7603 4.0 62.3 1.0 CE D:MET517 4.1 37.6 1.0 C D:ILE515 4.3 44.6 1.0 C20 D:OE7603 4.6 62.1 1.0 N D:MET517 4.9 40.9 1.0 CG D:LYS284 4.9 52.8 1.0 OG1 D:THR514 4.9 64.4 1.0

Chlorine binding site 5 out of 5 in the Crystal Structure of Ts-Dhfr From Cryptosporidium Hominis in Complex with Nadph, Fdump and 2-(4-((2-Amino-4-Oxo-4,7-Dihydro-3H-Pyrrolo[2, 3-D]Pyrimidin-5-Yl)Methyl)Benzamido)-4-Chlorobenzoic Acid


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 5 of Crystal Structure of Ts-Dhfr From Cryptosporidium Hominis in Complex with Nadph, Fdump and 2-(4-((2-Amino-4-Oxo-4,7-Dihydro-3H-Pyrrolo[2, 3-D]Pyrimidin-5-Yl)Methyl)Benzamido)-4-Chlorobenzoic Acid within 5.0Å range: probe atom residue distance (Å) B Occ E:Cl603 b:0.3 occ:1.00 CL1 E:OE7603 0.0 0.3 1.0 C17 E:OE7603 1.7 89.6 1.0 C16 E:OE7603 2.7 75.4 1.0 C18 E:OE7603 2.7 99.9 1.0 O E:ILE515 3.1 66.0 1.0 NZ E:LYS284 3.6 49.0 1.0 CD E:LYS284 3.9 64.3 1.0 CE E:LYS284 4.0 56.5 1.0 C19 E:OE7603 4.0 91.7 1.0 C15 E:OE7603 4.0 77.9 1.0 CD2 E:LEU429 4.1 62.7 1.0 CE E:MET517 4.1 66.5 1.0 C E:ILE515 4.2 64.0 1.0 C20 E:OE7603 4.6 87.9 1.0 OG1 E:THR514 4.7 81.1 1.0 N E:MET517 4.8 57.4 1.0 CG E:LYS284 4.8 69.9 1.0 N E:ILE515 4.9 74.8 1.0

D.J.Czyzyk, M.Valhondo, L.Deiana, J.Tirado-Rives, W.L.Jorgensen, K.S.Anderson. Structure Activity Relationship Towards Design of Cryptosporidium Specific Thymidylate Synthase Inhibitors. Eur.J.Med.Chem. V. 183 11673 2019.
ISSN: ISSN 0223-5234
PubMed: 31536894
DOI: 10.1016/J.EJMECH.2019.111673