Fluorine in PDB 6pfg: 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-Carbamoylbenzoic 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-Carbamoylbenzoic Acid., PDB code: 6pfg 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)	48.64 / 2.71
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	213.635, 116.595, 221.411, 90.00, 95.21, 90.00
R / Rfree (%)	20.1 / 23.1

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-Carbamoylbenzoic Acid. (pdb code 6pfg). 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-Carbamoylbenzoic Acid., PDB code: 6pfg:
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-Carbamoylbenzoic 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-Carbamoylbenzoic Acid. within 5.0Å range: probe atom residue distance (Å) B Occ A:F602 b:81.3 occ:1.00 F5 A:UFP602 0.0 81.3 1.0 C5 A:UFP602 1.4 84.7 1.0 C6 A:UFP602 2.3 84.0 1.0 C4 A:UFP602 2.4 74.0 1.0 O4 A:UFP602 2.7 59.1 1.0 C6 A:OFJ603 3.2 83.2 1.0 C5 A:OFJ603 3.2 84.7 1.0 N1 A:UFP602 3.6 77.2 1.0 N3 A:UFP602 3.6 71.9 1.0 N3 A:OFJ603 3.6 90.1 1.0 C7 A:OFJ603 3.7 77.4 1.0 C2 A:OFJ603 3.7 95.3 1.0 OH A:TYR342 4.0 72.5 1.0 C1 A:OFJ603 4.0 87.0 1.0 C2 A:UFP602 4.1 67.7 1.0 CZ2 A:TRP316 4.1 73.4 1.0 SG A:CYS402 4.1 73.0 1.0 CH2 A:TRP316 4.1 79.0 1.0 CE2 A:TYR342 4.4 47.0 1.0 CB A:CYS402 4.4 54.5 1.0 CZ A:TYR342 4.6 45.7 1.0 O4' A:UFP602 4.6 79.1 1.0 C3 A:OFJ603 4.7 91.4 1.0 CD2 A:LEU399 4.7 85.1 1.0 C1' A:UFP602 4.7 71.2 1.0 N1 A:OFJ603 5.0 88.1 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-Carbamoylbenzoic 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-Carbamoylbenzoic Acid. within 5.0Å range: probe atom residue distance (Å) B Occ B:F602 b:72.3 occ:1.00 F5 B:UFP602 0.0 72.3 1.0 C5 B:UFP602 1.4 66.1 1.0 C6 B:UFP602 2.3 62.1 1.0 C4 B:UFP602 2.4 67.0 1.0 O4 B:UFP602 2.7 61.8 1.0 C5 B:OFJ603 3.0 68.3 1.0 C6 B:OFJ603 3.1 68.3 1.0 C7 B:OFJ603 3.5 62.3 1.0 N3 B:OFJ603 3.6 70.5 1.0 N1 B:UFP602 3.6 60.3 1.0 C2 B:OFJ603 3.6 70.1 1.0 N3 B:UFP602 3.6 61.9 1.0 O B:HOH727 3.9 41.4 1.0 C1 B:OFJ603 3.9 63.0 1.0 C2 B:UFP602 4.1 58.6 1.0 OH B:TYR342 4.1 53.8 1.0 CZ2 B:TRP316 4.1 50.1 1.0 CH2 B:TRP316 4.1 48.9 1.0 SG B:CYS402 4.1 61.9 1.0 O B:HOH779 4.4 47.8 1.0 CD2 B:LEU399 4.5 44.0 1.0 CE2 B:TYR342 4.5 50.3 1.0 C3 B:OFJ603 4.5 67.3 1.0 CB B:CYS402 4.5 45.0 1.0 O4' B:UFP602 4.6 58.6 1.0 C1' B:UFP602 4.7 53.0 1.0 CZ B:TYR342 4.8 50.3 1.0 N1 B:OFJ603 4.9 71.0 1.0 O2 B:OFJ603 4.9 71.7 1.0 C8 B:OFJ603 4.9 53.9 1.0 CE2 B:TRP316 5.0 39.5 1.0 CZ3 B:TRP316 5.0 39.6 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-Carbamoylbenzoic 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-Carbamoylbenzoic Acid. within 5.0Å range: probe atom residue distance (Å) B Occ C:F602 b:80.3 occ:1.00 F5 C:UFP602 0.0 80.3 1.0 C5 C:UFP602 1.4 70.1 1.0 C6 C:UFP602 2.3 70.1 1.0 C4 C:UFP602 2.4 62.1 1.0 O4 C:UFP602 2.7 65.5 1.0 O C:HOH711 3.5 54.2 1.0 C6 C:OFJ603 3.6 75.4 1.0 C5 C:OFJ603 3.6 75.4 1.0 N1 C:UFP602 3.6 70.1 1.0 N3 C:UFP602 3.6 58.8 1.0 OH C:TYR342 3.8 60.5 1.0 C7 C:OFJ603 3.9 78.9 1.0 SG C:CYS402 4.0 61.0 1.0 N3 C:OFJ603 4.1 82.3 1.0 C2 C:UFP602 4.1 59.7 1.0 C2 C:OFJ603 4.1 86.9 1.0 CB C:CYS402 4.1 48.1 1.0 CH2 C:TRP316 4.3 68.5 1.0 CZ2 C:TRP316 4.3 78.0 1.0 CE2 C:TYR342 4.3 46.0 1.0 C1 C:OFJ603 4.4 78.3 1.0 CZ C:TYR342 4.5 41.7 1.0 O4' C:UFP602 4.7 63.6 1.0 C1' C:UFP602 4.8 69.5 1.0 CD2 C:HIS403 4.8 52.6 1.0 CD2 C:LEU399 4.9 74.4 1.0 NE2 C:HIS403 4.9 60.2 1.0 C3 C:OFJ603 5.0 75.7 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 2-(4-((2-Amino-4-Oxo-4,7-Dihydro-3H-Pyrrolo[2, 3-D]Pyrimidin-5-Yl)Methyl)Benzamido)-4-Carbamoylbenzoic 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-Carbamoylbenzoic Acid. within 5.0Å range: probe atom residue distance (Å) B Occ D:F602 b:99.5 occ:1.00 F5 D:UFP602 0.0 99.5 1.0 C5 D:UFP602 1.4 95.6 1.0 C6 D:UFP602 2.3 97.5 1.0 C4 D:UFP602 2.4 94.6 1.0 O4 D:UFP602 2.7 97.1 1.0 C5 D:OFJ603 3.3 0.1 1.0 C6 D:OFJ603 3.3 0.2 1.0 N1 D:UFP602 3.6 96.9 1.0 C7 D:OFJ603 3.6 98.2 1.0 N3 D:UFP602 3.6 93.0 1.0 C2 D:OFJ603 3.8 0.9 1.0 N3 D:OFJ603 3.8 0.3 1.0 CH2 D:TRP316 4.0 90.1 1.0 CZ2 D:TRP316 4.0 97.2 1.0 OH D:TYR342 4.0 88.6 1.0 C1 D:OFJ603 4.1 0.4 1.0 C2 D:UFP602 4.1 91.5 1.0 SG D:CYS402 4.3 96.6 1.0 CE2 D:TYR342 4.4 82.0 1.0 CB D:CYS402 4.6 66.0 1.0 C3 D:OFJ603 4.6 0.9 1.0 O4' D:UFP602 4.6 0.7 1.0 CZ D:TYR342 4.6 78.7 1.0 CD2 D:LEU399 4.7 0.4 1.0 C1' D:UFP602 4.7 94.8 1.0 CZ3 D:TRP316 4.9 93.8 1.0 CE2 D:TRP316 4.9 99.2 1.0 O2 D:OFJ603 5.0 0.4 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-Carbamoylbenzoic 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-Carbamoylbenzoic Acid. within 5.0Å range: probe atom residue distance (Å) B Occ E:F602 b:67.9 occ:1.00 F5 E:UFP602 0.0 67.9 1.0 C5 E:UFP602 1.4 63.5 1.0 C6 E:UFP602 2.3 62.9 1.0 C4 E:UFP602 2.4 55.6 1.0 O4 E:UFP602 2.7 40.0 1.0 C5 E:OFJ603 3.2 59.9 1.0 C6 E:OFJ603 3.2 55.3 1.0 C7 E:OFJ603 3.6 56.2 1.0 N1 E:UFP602 3.6 49.7 1.0 N3 E:UFP602 3.6 62.6 1.0 C2 E:OFJ603 3.6 67.5 1.0 O E:HOH734 3.7 36.5 1.0 N3 E:OFJ603 3.7 70.0 1.0 C1 E:OFJ603 3.9 58.7 1.0 OH E:TYR342 4.0 48.0 1.0 O E:HOH826 4.1 46.7 1.0 C2 E:UFP602 4.1 47.0 1.0 SG E:CYS402 4.1 52.3 1.0 CZ2 E:TRP316 4.2 36.0 1.0 CH2 E:TRP316 4.3 43.9 1.0 CB E:CYS402 4.4 39.6 1.0 C3 E:OFJ603 4.5 65.8 1.0 CE2 E:TYR342 4.5 40.0 1.0 O4' E:UFP602 4.6 49.7 1.0 CZ E:TYR342 4.7 42.3 1.0 C1' E:UFP602 4.7 46.4 1.0 CD2 E:LEU399 4.8 46.3 1.0 O2 E:OFJ603 4.9 63.3 1.0 N1 E:OFJ603 4.9 42.6 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