Fluorine in PDB 6pfa: 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)Methyl)Benzoic 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)Methyl)Benzoic Acid., PDB code: 6pfa 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)	48.93 / 2.79
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	213.210, 117.294, 222.817, 90.00, 95.72, 90.00
R / Rfree (%)	22.1 / 24.9

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)Methyl)Benzoic Acid. (pdb code 6pfa). 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)Methyl)Benzoic Acid., PDB code: 6pfa:
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)Methyl)Benzoic 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)Methyl)Benzoic Acid. within 5.0Å range: probe atom residue distance (Å) B Occ A:F602 b:92.7 occ:1.00 F5 A:UFP602 0.0 92.7 1.0 C5 A:UFP602 1.4 84.8 1.0 C6 A:UFP602 2.3 78.7 1.0 C4 A:UFP602 2.4 84.5 1.0 O4 A:UFP602 2.7 88.7 1.0 C6 A:OF4603 3.2 85.1 1.0 C5 A:OF4603 3.3 83.2 1.0 N1 A:UFP602 3.6 85.4 1.0 N3 A:UFP602 3.6 81.0 1.0 C7 A:OF4603 3.6 88.1 1.0 OH A:TYR342 3.7 68.0 1.0 N3 A:OF4603 3.8 85.8 1.0 SG A:CYS402 3.9 77.5 1.0 C2 A:OF4603 4.0 93.8 1.0 C2 A:UFP602 4.1 76.2 1.0 CH2 A:TRP316 4.2 85.8 1.0 C1 A:OF4603 4.2 80.7 1.0 CZ2 A:TRP316 4.2 89.8 1.0 CB A:CYS402 4.2 61.0 1.0 CE2 A:TYR342 4.4 66.8 1.0 CZ A:TYR342 4.5 57.8 1.0 O4' A:UFP602 4.6 77.4 1.0 C1' A:UFP602 4.7 78.5 1.0 CD2 A:HIS403 4.9 69.8 1.0 NE2 A:HIS403 4.9 72.4 1.0 C3 A:OF4603 4.9 84.8 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)Methyl)Benzoic 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)Methyl)Benzoic Acid. within 5.0Å range: probe atom residue distance (Å) B Occ B:F602 b:69.0 occ:1.00 F5 B:UFP602 0.0 69.0 1.0 C5 B:UFP602 1.4 67.3 1.0 C6 B:UFP602 2.3 72.1 1.0 C4 B:UFP602 2.4 69.6 1.0 O4 B:UFP602 2.8 53.3 1.0 C5 B:OF4603 3.0 64.7 1.0 C6 B:OF4603 3.1 68.7 1.0 C7 B:OF4603 3.2 63.2 1.0 N1 B:UFP602 3.6 66.1 1.0 N3 B:UFP602 3.6 75.2 1.0 C2 B:OF4603 3.6 77.3 1.0 N3 B:OF4603 3.8 71.2 1.0 SG B:CYS402 3.9 68.2 1.0 OH B:TYR342 4.0 65.2 1.0 C1 B:OF4603 4.1 65.9 1.0 C2 B:UFP602 4.1 66.0 1.0 CH2 B:TRP316 4.2 55.8 1.0 CZ2 B:TRP316 4.2 56.9 1.0 CB B:CYS402 4.3 59.3 1.0 C3 B:OF4603 4.5 71.9 1.0 O4' B:UFP602 4.6 61.0 1.0 C8 B:OF4603 4.7 60.6 1.0 CE2 B:TYR342 4.7 55.6 1.0 C1' B:UFP602 4.7 61.9 1.0 CZ B:TYR342 4.7 55.6 1.0 O1 B:OF4603 4.8 67.3 1.0 CD2 B:LEU399 4.9 52.1 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)Methyl)Benzoic 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)Methyl)Benzoic Acid. within 5.0Å range: probe atom residue distance (Å) B Occ C:F602 b:98.7 occ:1.00 F5 C:UFP602 0.0 98.7 1.0 C5 C:UFP602 1.4 94.5 1.0 C6 C:UFP602 2.3 97.0 1.0 C4 C:UFP602 2.4 93.4 1.0 O4 C:UFP602 2.7 85.2 1.0 C6 C:OF4603 3.0 88.4 1.0 C5 C:OF4603 3.1 90.3 1.0 C7 C:OF4603 3.5 95.0 1.0 N1 C:UFP602 3.6 98.6 1.0 N3 C:UFP602 3.6 90.1 1.0 N3 C:OF4603 3.7 96.0 1.0 C2 C:OF4603 3.8 0.1 1.0 OH C:TYR342 3.9 88.5 1.0 SG C:CYS402 3.9 85.1 1.0 C1 C:OF4603 4.1 0.4 1.0 C2 C:UFP602 4.1 85.0 1.0 CH2 C:TRP316 4.3 92.2 1.0 CZ2 C:TRP316 4.3 88.1 1.0 CB C:CYS402 4.3 70.8 1.0 CE2 C:TYR342 4.6 75.5 1.0 O4' C:UFP602 4.6 98.5 1.0 CZ C:TYR342 4.7 73.7 1.0 C1' C:UFP602 4.7 93.9 1.0 C3 C:OF4603 4.8 0.2 1.0 NE2 C:HIS403 4.8 83.5 1.0 CD2 C:HIS403 4.9 76.7 1.0 C8 C:OF4603 5.0 87.0 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)Methyl)Benzoic 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)Methyl)Benzoic Acid. within 5.0Å range: probe atom residue distance (Å) B Occ D:F602 b:77.7 occ:1.00 F5 D:UFP602 0.0 77.7 1.0 C5 D:UFP602 1.4 74.0 1.0 C6 D:UFP602 2.3 71.9 1.0 C4 D:UFP602 2.4 75.2 1.0 O4 D:UFP602 2.7 70.5 1.0 C5 D:OF4603 3.0 67.6 1.0 C6 D:OF4603 3.0 66.0 1.0 C7 D:OF4603 3.2 73.8 1.0 N1 D:UFP602 3.6 73.8 1.0 N3 D:UFP602 3.6 76.3 1.0 C2 D:OF4603 3.7 81.2 1.0 N3 D:OF4603 3.7 77.7 1.0 OH D:TYR342 3.9 81.1 1.0 SG D:CYS402 3.9 77.8 1.0 CH2 D:TRP316 4.0 59.1 1.0 CZ2 D:TRP316 4.0 65.4 1.0 C2 D:UFP602 4.1 72.2 1.0 C1 D:OF4603 4.1 76.5 1.0 CB D:CYS402 4.4 65.0 1.0 CE2 D:TYR342 4.6 64.1 1.0 O4' D:UFP602 4.6 71.2 1.0 C3 D:OF4603 4.7 76.4 1.0 CZ D:TYR342 4.7 59.6 1.0 C1' D:UFP602 4.7 72.8 1.0 C8 D:OF4603 4.7 67.2 1.0 CD2 D:LEU399 4.7 61.7 1.0 CZ3 D:TRP316 4.9 59.1 1.0 CE2 D:TRP316 5.0 61.3 1.0 O1 D:OF4603 5.0 80.8 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)Methyl)Benzoic 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)Methyl)Benzoic Acid. within 5.0Å range: probe atom residue distance (Å) B Occ E:F602 b:0.3 occ:1.00 F5 E:UFP602 0.0 0.3 1.0 C5 E:UFP602 1.4 0.5 1.0 C6 E:UFP602 2.3 0.3 1.0 C4 E:UFP602 2.4 0.7 1.0 O4 E:UFP602 2.7 0.8 1.0 C6 E:OF4603 3.1 0.7 1.0 C5 E:OF4603 3.2 0.1 1.0 C7 E:OF4603 3.4 0.7 1.0 N1 E:UFP602 3.6 0.1 1.0 N3 E:UFP602 3.6 0.9 1.0 CH2 E:TRP316 3.8 0.2 1.0 CZ2 E:TRP316 3.9 0.2 1.0 N3 E:OF4603 3.9 0.4 1.0 OH E:TYR342 4.0 0.1 1.0 C2 E:OF4603 4.0 0.2 1.0 C2 E:UFP602 4.1 0.3 1.0 SG E:CYS402 4.2 0.8 1.0 C1 E:OF4603 4.4 0.7 1.0 CE2 E:TYR342 4.4 0.2 1.0 CZ E:TYR342 4.6 99.1 1.0 O4' E:UFP602 4.6 0.1 1.0 CZ3 E:TRP316 4.7 0.0 1.0 CD2 E:LEU399 4.7 0.8 1.0 CB E:CYS402 4.7 91.3 1.0 C1' E:UFP602 4.7 0.8 1.0 CE2 E:TRP316 4.8 0.9 1.0 C8 E:OF4603 4.9 0.3 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