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

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

Resolution Low / High (Å)	48.59 / 2.89
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	213.380, 116.741, 221.580, 90.00, 95.05, 90.00
R / Rfree (%)	21.2 / 25.2

The binding sites of Fluorine atom in the Crystal Structure of Ts-Dhfr From Cryptosporidium Hominis in Complex with Nadph, Fdump and 3-(4-((2-Amino-4-Oxo-4,7-Dihydro-3H-Pyrrolo[2, 3-D]Pyrimidin-5-Yl)Methyl)Benzamido)-4-(Carboxymethyl)Benzoic Acid. (pdb code 6pfi). 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 3-(4-((2-Amino-4-Oxo-4,7-Dihydro-3H-Pyrrolo[2, 3-D]Pyrimidin-5-Yl)Methyl)Benzamido)-4-(Carboxymethyl)Benzoic Acid., PDB code: 6pfi:
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 3-(4-((2-Amino-4-Oxo-4,7-Dihydro-3H-Pyrrolo[2, 3-D]Pyrimidin-5-Yl)Methyl)Benzamido)-4-(Carboxymethyl)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 3-(4-((2-Amino-4-Oxo-4,7-Dihydro-3H-Pyrrolo[2, 3-D]Pyrimidin-5-Yl)Methyl)Benzamido)-4-(Carboxymethyl)Benzoic Acid. within 5.0Å range: probe atom residue distance (Å) B Occ A:F602 b:92.8 occ:1.00 F5 A:UFP602 0.0 92.8 1.0 C5 A:UFP602 1.4 85.3 1.0 C6 A:UFP602 2.3 79.1 1.0 C4 A:UFP602 2.4 79.6 1.0 O4 A:UFP602 2.7 82.0 1.0 C6 A:OEP603 3.2 82.6 1.0 C5 A:OEP603 3.2 71.4 1.0 C7 A:OEP603 3.5 79.9 1.0 N1 A:UFP602 3.6 76.4 1.0 N3 A:UFP602 3.6 84.9 1.0 N3 A:OEP603 3.8 83.4 1.0 C2 A:OEP603 3.8 80.6 1.0 OH A:TYR342 3.9 75.9 1.0 SG A:CYS402 4.1 74.5 1.0 C2 A:UFP602 4.1 78.0 1.0 C1 A:OEP603 4.1 75.0 1.0 CZ2 A:TRP316 4.1 85.0 1.0 CH2 A:TRP316 4.2 73.5 1.0 CB A:CYS402 4.5 61.1 1.0 CE2 A:TYR342 4.6 86.0 1.0 O4' A:UFP602 4.6 74.3 1.0 CZ A:TYR342 4.6 74.9 1.0 CD2 A:LEU399 4.7 70.5 1.0 C1' A:UFP602 4.7 74.0 1.0 C3 A:OEP603 4.7 90.3 1.0 C8 A:OEP603 4.9 69.3 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 3-(4-((2-Amino-4-Oxo-4,7-Dihydro-3H-Pyrrolo[2, 3-D]Pyrimidin-5-Yl)Methyl)Benzamido)-4-(Carboxymethyl)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 3-(4-((2-Amino-4-Oxo-4,7-Dihydro-3H-Pyrrolo[2, 3-D]Pyrimidin-5-Yl)Methyl)Benzamido)-4-(Carboxymethyl)Benzoic Acid. within 5.0Å range: probe atom residue distance (Å) B Occ B:F602 b:79.2 occ:1.00 F5 B:UFP602 0.0 79.2 1.0 C5 B:UFP602 1.4 68.6 1.0 C6 B:UFP602 2.3 70.5 1.0 C4 B:UFP602 2.4 70.0 1.0 O4 B:UFP602 2.7 58.8 1.0 C5 B:OEP603 3.1 66.0 1.0 C7 B:OEP603 3.2 63.1 1.0 C6 B:OEP603 3.3 71.2 1.0 N1 B:UFP602 3.6 75.2 1.0 N3 B:UFP602 3.6 71.8 1.0 C2 B:OEP603 3.8 78.8 1.0 SG B:CYS402 3.9 69.9 1.0 N3 B:OEP603 4.0 75.9 1.0 OH B:TYR342 4.0 79.7 1.0 C2 B:UFP602 4.1 75.2 1.0 CZ2 B:TRP316 4.1 63.6 1.0 CH2 B:TRP316 4.2 53.9 1.0 C1 B:OEP603 4.2 73.1 1.0 CB B:CYS402 4.4 65.7 1.0 O4' B:UFP602 4.6 65.3 1.0 C3 B:OEP603 4.6 79.4 1.0 CE2 B:TYR342 4.7 71.2 1.0 C8 B:OEP603 4.7 65.9 1.0 CZ B:TYR342 4.7 69.9 1.0 C1' B:UFP602 4.7 65.1 1.0 CD2 B:LEU399 4.7 57.1 1.0 O1 B:OEP603 4.9 85.5 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 3-(4-((2-Amino-4-Oxo-4,7-Dihydro-3H-Pyrrolo[2, 3-D]Pyrimidin-5-Yl)Methyl)Benzamido)-4-(Carboxymethyl)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 3-(4-((2-Amino-4-Oxo-4,7-Dihydro-3H-Pyrrolo[2, 3-D]Pyrimidin-5-Yl)Methyl)Benzamido)-4-(Carboxymethyl)Benzoic Acid. within 5.0Å range: probe atom residue distance (Å) B Occ C:F602 b:0.7 occ:1.00 F5 C:UFP602 0.0 0.7 1.0 C5 C:UFP602 1.4 90.0 1.0 C6 C:UFP602 2.3 88.2 1.0 C4 C:UFP602 2.4 85.2 1.0 O4 C:UFP602 2.7 90.9 1.0 C5 C:OEP603 3.2 81.8 1.0 C7 C:OEP603 3.3 87.7 1.0 C6 C:OEP603 3.4 81.9 1.0 N1 C:UFP602 3.6 87.0 1.0 N3 C:UFP602 3.6 86.9 1.0 C2 C:OEP603 3.8 88.0 1.0 OH C:TYR342 3.9 81.2 1.0 N3 C:OEP603 4.0 80.8 1.0 SG C:CYS402 4.0 78.8 1.0 CH2 C:TRP316 4.1 73.8 1.0 CZ2 C:TRP316 4.1 87.9 1.0 C2 C:UFP602 4.1 82.4 1.0 C1 C:OEP603 4.2 79.2 1.0 CB C:CYS402 4.4 76.6 1.0 CE2 C:TYR342 4.5 85.3 1.0 C3 C:OEP603 4.6 91.0 1.0 O4' C:UFP602 4.6 76.8 1.0 CZ C:TYR342 4.6 77.3 1.0 C1' C:UFP602 4.7 80.9 1.0 C8 C:OEP603 4.8 83.0 1.0 CD2 C:LEU399 4.9 74.8 1.0 O1 C:OEP603 4.9 90.7 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 3-(4-((2-Amino-4-Oxo-4,7-Dihydro-3H-Pyrrolo[2, 3-D]Pyrimidin-5-Yl)Methyl)Benzamido)-4-(Carboxymethyl)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 3-(4-((2-Amino-4-Oxo-4,7-Dihydro-3H-Pyrrolo[2, 3-D]Pyrimidin-5-Yl)Methyl)Benzamido)-4-(Carboxymethyl)Benzoic Acid. within 5.0Å range: probe atom residue distance (Å) B Occ D:F602 b:78.6 occ:1.00 F5 D:UFP602 0.0 78.6 1.0 C5 D:UFP602 1.4 66.3 1.0 C6 D:UFP602 2.3 68.8 1.0 C4 D:UFP602 2.4 80.1 1.0 O4 D:UFP602 2.8 65.7 1.0 C5 D:OEP603 3.1 69.0 1.0 C7 D:OEP603 3.3 65.8 1.0 C6 D:OEP603 3.3 85.7 1.0 N1 D:UFP602 3.6 77.6 1.0 N3 D:UFP602 3.6 71.6 1.0 C2 D:OEP603 3.8 83.2 1.0 OH D:TYR342 3.8 81.2 1.0 N3 D:OEP603 4.0 71.8 1.0 SG D:CYS402 4.0 76.5 1.0 CZ2 D:TRP316 4.1 75.7 1.0 C2 D:UFP602 4.1 66.6 1.0 CH2 D:TRP316 4.1 63.9 1.0 C1 D:OEP603 4.2 70.7 1.0 CB D:CYS402 4.4 61.9 1.0 CE2 D:TYR342 4.5 77.4 1.0 CD2 D:LEU399 4.5 62.7 1.0 CZ D:TYR342 4.5 77.6 1.0 O4' D:UFP602 4.6 62.4 1.0 C3 D:OEP603 4.6 83.6 1.0 C8 D:OEP603 4.7 66.9 1.0 C1' D:UFP602 4.7 70.0 1.0 O1 D:OEP603 4.9 87.2 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 3-(4-((2-Amino-4-Oxo-4,7-Dihydro-3H-Pyrrolo[2, 3-D]Pyrimidin-5-Yl)Methyl)Benzamido)-4-(Carboxymethyl)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 3-(4-((2-Amino-4-Oxo-4,7-Dihydro-3H-Pyrrolo[2, 3-D]Pyrimidin-5-Yl)Methyl)Benzamido)-4-(Carboxymethyl)Benzoic Acid. within 5.0Å range: probe atom residue distance (Å) B Occ E:F602 b:0.1 occ:1.00 F5 E:UFP602 0.0 0.1 1.0 C5 E:UFP602 1.4 93.9 1.0 C6 E:UFP602 2.3 0.1 1.0 C4 E:UFP602 2.4 86.3 1.0 O4 E:UFP602 2.7 90.9 1.0 C5 E:OEP603 3.2 98.1 1.0 C6 E:OEP603 3.3 0.6 1.0 C7 E:OEP603 3.5 94.6 1.0 N1 E:UFP602 3.6 0.9 1.0 N3 E:UFP602 3.6 94.8 1.0 C2 E:OEP603 3.9 0.8 1.0 OH E:TYR342 3.9 96.3 1.0 N3 E:OEP603 3.9 94.9 1.0 SG E:CYS402 4.0 98.0 1.0 C2 E:UFP602 4.1 87.9 1.0 CH2 E:TRP316 4.2 0.5 1.0 C1 E:OEP603 4.2 91.2 1.0 CZ2 E:TRP316 4.2 0.6 1.0 CD2 E:LEU399 4.4 92.5 1.0 CE2 E:TYR342 4.5 94.9 1.0 CB E:CYS402 4.5 76.8 1.0 CZ E:TYR342 4.6 84.4 1.0 O4' E:UFP602 4.6 98.7 1.0 C1' E:UFP602 4.7 0.4 1.0 C3 E:OEP603 4.8 99.9 1.0 C8 E:OEP603 5.0 82.9 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