Fluorine in PDB 6pfd: 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)Terephthalic 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)Terephthalic Acid., PDB code: 6pfd 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)	48.43 / 3.32
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	213.033, 115.887, 220.808, 90.00, 95.05, 90.00
R / Rfree (%)	22 / 26.2

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)Terephthalic Acid. (pdb code 6pfd). 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)Terephthalic Acid., PDB code: 6pfd:
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)Terephthalic 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)Terephthalic Acid. within 5.0Å range: probe atom residue distance (Å) B Occ A:F602 b:99.6 occ:1.00 F5 A:UFP602 0.0 99.6 1.0 C5 A:UFP602 1.4 86.3 1.0 C6 A:UFP602 2.3 77.0 1.0 C4 A:UFP602 2.4 94.6 1.0 O4 A:UFP602 2.7 0.5 1.0 C5 A:OEJ603 3.3 79.4 1.0 C7 A:OEJ603 3.4 65.2 1.0 C6 A:OEJ603 3.5 72.9 1.0 N1 A:UFP602 3.6 78.6 1.0 N3 A:UFP602 3.6 83.7 1.0 C2 A:OEJ603 3.9 93.0 1.0 CH2 A:TRP316 3.9 62.3 1.0 CZ2 A:TRP316 3.9 62.0 1.0 OH A:TYR342 4.0 76.6 1.0 N3 A:OEJ603 4.1 89.8 1.0 C2 A:UFP602 4.1 77.5 1.0 SG A:CYS402 4.2 69.2 1.0 C1 A:OEJ603 4.3 90.5 1.0 CE2 A:TYR342 4.4 78.6 1.0 CB A:CYS402 4.6 64.5 1.0 CZ A:TYR342 4.6 65.6 1.0 O4' A:UFP602 4.6 75.0 1.0 CD2 A:LEU399 4.7 75.1 1.0 C3 A:OEJ603 4.7 89.4 1.0 C1' A:UFP602 4.7 63.3 1.0 CZ3 A:TRP316 4.8 62.2 1.0 CE2 A:TRP316 4.9 65.5 1.0 C8 A:OEJ603 4.9 71.2 1.0 O1 A:OEJ603 4.9 83.7 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)Terephthalic 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)Terephthalic Acid. within 5.0Å range: probe atom residue distance (Å) B Occ B:F602 b:0.0 occ:1.00 F5 B:UFP602 0.0 0.0 1.0 C5 B:UFP602 1.4 0.2 1.0 C6 B:UFP602 2.4 0.9 1.0 C4 B:UFP602 2.4 0.4 1.0 O4 B:UFP602 2.7 0.2 1.0 C5 B:OEJ603 3.6 0.8 1.0 C6 B:OEJ603 3.6 0.9 1.0 N1 B:UFP602 3.6 99.5 1.0 N3 B:UFP602 3.6 0.8 1.0 OH B:TYR342 3.7 92.6 1.0 C7 B:OEJ603 3.9 0.6 1.0 SG B:CYS402 4.1 95.0 1.0 C2 B:UFP602 4.1 95.0 1.0 C2 B:OEJ603 4.1 0.1 1.0 N3 B:OEJ603 4.1 0.5 1.0 CZ2 B:TRP316 4.2 0.0 1.0 CB B:CYS402 4.2 70.8 1.0 CE2 B:TYR342 4.3 94.2 1.0 CH2 B:TRP316 4.3 0.9 1.0 CZ B:TYR342 4.3 89.5 1.0 C1 B:OEJ603 4.4 0.2 1.0 O4' B:UFP602 4.7 0.7 1.0 CD2 B:HIS403 4.7 77.4 1.0 C1' B:UFP602 4.8 94.8 1.0 CD2 B:LEU399 4.8 93.9 1.0 NE2 B:HIS403 4.9 82.8 1.0 C3 B:OEJ603 5.0 0.8 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)Terephthalic 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)Terephthalic Acid. within 5.0Å range: probe atom residue distance (Å) B Occ C:F602 b:0.9 occ:1.00 F5 C:UFP602 0.0 0.9 1.0 C5 C:UFP602 1.4 86.5 1.0 C6 C:UFP602 2.3 81.8 1.0 C4 C:UFP602 2.4 88.7 1.0 O4 C:UFP602 2.7 85.9 1.0 C5 C:OEJ603 3.1 79.4 1.0 C7 C:OEJ603 3.2 77.0 1.0 C6 C:OEJ603 3.2 75.5 1.0 N1 C:UFP602 3.6 86.3 1.0 N3 C:UFP602 3.6 90.7 1.0 C2 C:OEJ603 3.7 0.2 1.0 CZ2 C:TRP316 3.8 78.4 1.0 N3 C:OEJ603 3.9 0.4 1.0 CH2 C:TRP316 3.9 68.8 1.0 OH C:TYR342 4.1 87.5 1.0 C2 C:UFP602 4.1 85.8 1.0 C1 C:OEJ603 4.2 0.1 1.0 SG C:CYS402 4.3 88.4 1.0 CD2 C:LEU399 4.3 86.1 1.0 CE2 C:TYR342 4.3 77.9 1.0 C3 C:OEJ603 4.6 97.4 1.0 O4' C:UFP602 4.6 90.9 1.0 CZ C:TYR342 4.6 78.4 1.0 CE2 C:TRP316 4.7 64.7 1.0 C8 C:OEJ603 4.7 88.0 1.0 C1' C:UFP602 4.7 81.1 1.0 CB C:CYS402 4.8 69.5 1.0 O1 C:OEJ603 4.8 99.0 1.0 CZ3 C:TRP316 4.9 59.5 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)Terephthalic 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)Terephthalic Acid. within 5.0Å range: probe atom residue distance (Å) B Occ D:F602 b:0.8 occ:1.00 F5 D:UFP602 0.0 0.8 1.0 C5 D:UFP602 1.4 0.5 1.0 C6 D:UFP602 2.4 0.7 1.0 C4 D:UFP602 2.4 0.6 1.0 O4 D:UFP602 2.7 0.4 1.0 C6 D:OEJ603 3.4 0.1 1.0 CZ2 D:TRP316 3.6 0.6 1.0 N1 D:UFP602 3.6 0.5 1.0 N3 D:UFP602 3.6 0.0 1.0 CH2 D:TRP316 3.7 99.6 1.0 OH D:TYR342 3.7 95.0 1.0 C5 D:OEJ603 3.7 0.6 1.0 CE2 D:TYR342 3.8 97.1 1.0 N3 D:OEJ603 3.9 0.4 1.0 C7 D:OEJ603 4.1 0.2 1.0 C2 D:UFP602 4.1 0.7 1.0 CZ D:TYR342 4.2 88.2 1.0 C2 D:OEJ603 4.3 0.2 1.0 SG D:CYS402 4.5 0.5 1.0 C1 D:OEJ603 4.5 0.2 1.0 CE2 D:TRP316 4.5 0.1 1.0 CD2 D:LEU399 4.6 0.7 1.0 CZ3 D:TRP316 4.7 0.8 1.0 O4' D:UFP602 4.7 0.6 1.0 CB D:CYS402 4.8 72.0 1.0 C1' D:UFP602 4.8 0.1 1.0 OE2 D:GLU294 4.8 98.3 1.0 NE2 D:HIS403 4.9 91.3 1.0 CD2 D:TYR342 4.9 0.8 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)Terephthalic 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)Terephthalic Acid. within 5.0Å range: probe atom residue distance (Å) B Occ E:F602 b:0.4 occ:1.00 F5 E:UFP602 0.0 0.4 1.0 C5 E:UFP602 1.4 0.7 1.0 C6 E:UFP602 2.3 0.9 1.0 C4 E:UFP602 2.4 0.3 1.0 O4 E:UFP602 2.7 0.6 1.0 C6 E:OEJ603 3.5 0.3 1.0 N1 E:UFP602 3.6 0.3 1.0 N3 E:UFP602 3.6 1.0 1.0 C5 E:OEJ603 3.7 0.9 1.0 OH E:TYR342 3.8 0.9 1.0 N3 E:OEJ603 3.9 0.1 1.0 CH2 E:TRP316 4.0 0.3 1.0 CZ2 E:TRP316 4.0 0.9 1.0 C2 E:UFP602 4.1 0.2 1.0 C2 E:OEJ603 4.1 0.7 1.0 CE2 E:TYR342 4.2 0.1 1.0 C7 E:OEJ603 4.2 0.8 1.0 C1 E:OEJ603 4.2 0.7 1.0 CD2 E:LEU399 4.2 0.1 1.0 SG E:CYS402 4.3 0.1 1.0 CZ E:TYR342 4.4 0.1 1.0 CB E:CYS402 4.6 0.5 1.0 O4' E:UFP602 4.7 0.9 1.0 C1' E:UFP602 4.8 1.0 1.0 CZ3 E:TRP316 4.9 0.8 1.0 CE2 E:TRP316 5.0 0.1 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