Fluorine 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:

Chlorine

(Cl)

5 atoms

The binding sites of Fluorine 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 Fluorine atom.
In total 5 binding sites of Fluorine 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 Fluorine binding site number: 1; 2; 3; 4; 5;

Fluorine 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 Fluorine with other atoms in the F 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:F602 b:62.2 occ:1.00 F5 A:UFP602 0.0 62.2 1.0 C5 A:UFP602 1.4 61.6 1.0 C6 A:UFP602 2.3 56.9 1.0 C4 A:UFP602 2.4 54.4 1.0 O4 A:UFP602 2.7 45.7 1.0 C5 A:OE7603 3.1 54.5 1.0 C6 A:OE7603 3.3 59.7 1.0 C7 A:OE7603 3.5 52.9 1.0 C2 A:OE7603 3.6 63.8 1.0 N1 A:UFP602 3.6 47.8 1.0 N3 A:UFP602 3.6 43.5 1.0 N3 A:OE7603 3.8 55.8 1.0 O A:HOH814 3.8 45.4 1.0 C1 A:OE7603 3.9 57.0 1.0 SG A:CYS402 4.1 55.5 1.0 C2 A:UFP602 4.1 47.0 1.0 OH A:TYR342 4.2 60.1 1.0 CZ2 A:TRP316 4.3 50.7 1.0 CH2 A:TRP316 4.4 56.9 1.0 C3 A:OE7603 4.4 62.7 1.0 CB A:CYS402 4.6 46.6 1.0 CE2 A:TYR342 4.6 43.4 1.0 O4' A:UFP602 4.7 46.1 1.0 CD2 A:LEU399 4.7 47.3 1.0 C1' A:UFP602 4.7 46.2 1.0 O1 A:OE7603 4.8 69.4 1.0 N1 A:OE7603 4.9 55.3 1.0 CZ A:TYR342 4.9 44.4 1.0 C8 A:OE7603 5.0 42.0 1.0

Fluorine 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 Fluorine with other atoms in the F 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:F602 b:57.4 occ:1.00 F5 B:UFP602 0.0 57.4 1.0 C5 B:UFP602 1.4 51.1 1.0 C6 B:UFP602 2.3 46.8 1.0 C4 B:UFP602 2.4 44.2 1.0 O4 B:UFP602 2.7 34.5 1.0 C5 B:OE7603 3.0 44.7 1.0 C6 B:OE7603 3.1 48.6 1.0 C7 B:OE7603 3.4 51.9 1.0 C2 B:OE7603 3.5 56.5 1.0 N1 B:UFP602 3.6 32.6 1.0 N3 B:UFP602 3.6 43.2 1.0 O B:HOH794 3.7 37.3 1.0 N3 B:OE7603 3.7 49.1 1.0 C1 B:OE7603 3.9 46.0 1.0 SG B:CYS402 4.0 52.5 1.0 C2 B:UFP602 4.1 38.7 1.0 CZ2 B:TRP316 4.2 39.7 1.0 CH2 B:TRP316 4.3 33.2 1.0 OH B:TYR342 4.3 53.0 1.0 C3 B:OE7603 4.4 52.7 1.0 O B:HOH852 4.4 36.8 1.0 CB B:CYS402 4.5 41.8 1.0 O4' B:UFP602 4.7 39.0 1.0 CD2 B:LEU399 4.7 37.1 1.0 O1 B:OE7603 4.7 54.9 1.0 CE2 B:TYR342 4.7 44.7 1.0 C1' B:UFP602 4.7 38.5 1.0 C8 B:OE7603 4.9 42.1 1.0 N1 B:OE7603 4.9 43.7 1.0 CZ B:TYR342 5.0 40.8 1.0

Fluorine 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 Fluorine with other atoms in the F 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:F602 b:62.0 occ:1.00 F5 C:UFP602 0.0 62.0 1.0 C5 C:UFP602 1.4 66.6 1.0 C6 C:UFP602 2.3 62.9 1.0 C4 C:UFP602 2.4 61.0 1.0 O4 C:UFP602 2.7 54.7 1.0 C5 C:OE7603 3.1 57.4 1.0 C6 C:OE7603 3.1 60.1 1.0 C2 C:OE7603 3.5 75.5 1.0 N3 C:OE7603 3.5 62.1 1.0 C7 C:OE7603 3.6 61.7 1.0 O C:HOH778 3.6 47.9 1.0 N1 C:UFP602 3.6 57.1 1.0 N3 C:UFP602 3.6 49.5 1.0 C1 C:OE7603 3.7 61.2 1.0 SG C:CYS402 4.1 58.6 1.0 C2 C:UFP602 4.1 54.8 1.0 CZ2 C:TRP316 4.2 49.6 1.0 CH2 C:TRP316 4.3 57.4 1.0 OH C:TYR342 4.3 61.1 1.0 C3 C:OE7603 4.4 70.9 1.0 CB C:CYS402 4.6 49.6 1.0 O4' C:UFP602 4.6 54.2 1.0 N1 C:OE7603 4.7 60.5 1.0 C1' C:UFP602 4.7 52.9 1.0 CE2 C:TYR342 4.8 52.2 1.0 O1 C:OE7603 4.8 74.7 1.0 CD2 C:LEU399 4.8 57.9 1.0

Fluorine 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 Fluorine with other atoms in the F 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:F602 b:63.1 occ:1.00 F5 D:UFP602 0.0 63.1 1.0 C5 D:UFP602 1.4 56.2 1.0 C6 D:UFP602 2.3 53.0 1.0 C4 D:UFP602 2.4 51.2 1.0 O4 D:UFP602 2.7 45.6 1.0 C5 D:OE7603 3.0 45.6 1.0 C6 D:OE7603 3.2 56.2 1.0 C7 D:OE7603 3.4 49.6 1.0 C2 D:OE7603 3.5 64.5 1.0 N1 D:UFP602 3.6 43.5 1.0 N3 D:UFP602 3.6 46.7 1.0 O D:HOH773 3.7 39.2 1.0 N3 D:OE7603 3.7 60.4 1.0 C1 D:OE7603 3.9 49.9 1.0 C2 D:UFP602 4.1 42.5 1.0 SG D:CYS402 4.1 55.9 1.0 CZ2 D:TRP316 4.3 43.4 1.0 OH D:TYR342 4.3 52.5 1.0 C3 D:OE7603 4.4 58.5 1.0 CH2 D:TRP316 4.4 41.0 1.0 CB D:CYS402 4.6 43.9 1.0 CD2 D:LEU399 4.6 38.5 1.0 O4' D:UFP602 4.6 41.9 1.0 O1 D:OE7603 4.7 65.7 1.0 CE2 D:TYR342 4.7 48.0 1.0 C1' D:UFP602 4.7 41.0 1.0 C8 D:OE7603 4.8 41.6 1.0 N1 D:OE7603 4.9 51.8 1.0 CZ D:TYR342 5.0 49.1 1.0

Fluorine 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 Fluorine with other atoms in the F 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:F602 b:67.8 occ:1.00 F5 E:UFP602 0.0 67.8 1.0 C5 E:UFP602 1.4 72.9 1.0 C6 E:UFP602 2.3 75.9 1.0 C4 E:UFP602 2.4 68.8 1.0 O4 E:UFP602 2.7 73.6 1.0 C5 E:OE7603 3.1 72.4 1.0 C6 E:OE7603 3.1 72.7 1.0 C7 E:OE7603 3.5 74.8 1.0 N1 E:UFP602 3.6 71.3 1.0 C2 E:OE7603 3.6 84.3 1.0 N3 E:OE7603 3.6 75.5 1.0 N3 E:UFP602 3.6 64.0 1.0 C1 E:OE7603 3.9 75.1 1.0 C2 E:UFP602 4.1 61.1 1.0 SG E:CYS402 4.1 80.5 1.0 OH E:TYR342 4.2 78.1 1.0 CZ2 E:TRP316 4.3 76.5 1.0 CH2 E:TRP316 4.3 73.7 1.0 C3 E:OE7603 4.5 77.9 1.0 CB E:CYS402 4.5 56.0 1.0 O4' E:UFP602 4.6 65.5 1.0 CE2 E:TYR342 4.7 68.4 1.0 C1' E:UFP602 4.7 69.5 1.0 CD2 E:LEU399 4.7 70.2 1.0 CZ E:TYR342 4.9 64.9 1.0 N1 E:OE7603 4.9 70.0 1.0 O1 E:OE7603 4.9 83.7 1.0 C8 E:OE7603 5.0 63.9 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