Fluorine in PDB 6pf7: 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)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)Benzoic Acid, PDB code: 6pf7 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)	49.10 / 2.80
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	214.774, 115.789, 220.142, 90.00, 94.68, 90.00
R / Rfree (%)	22.2 / 25.3

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)Benzoic Acid (pdb code 6pf7). 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)Benzoic Acid, PDB code: 6pf7:
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)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)Benzoic Acid within 5.0Å range: probe atom residue distance (Å) B Occ A:F602 b:76.2 occ:1.00 F5 A:UFP602 0.0 76.2 1.0 C5 A:UFP602 1.4 78.7 1.0 C6 A:UFP602 2.3 78.1 1.0 C4 A:UFP602 2.4 79.0 1.0 O4 A:UFP602 2.7 77.9 1.0 C05 A:OG7603 3.1 70.9 1.0 C06 A:OG7603 3.2 72.7 1.0 C07 A:OG7603 3.5 66.4 1.0 C02 A:OG7603 3.6 86.0 1.0 N1 A:UFP602 3.6 76.9 1.0 N3 A:UFP602 3.6 72.7 1.0 N03 A:OG7603 3.7 82.2 1.0 C01 A:OG7603 3.9 72.6 1.0 OH A:TYR342 4.0 66.7 1.0 CH2 A:TRP316 4.1 49.0 1.0 C2 A:UFP602 4.1 71.0 1.0 SG A:CYS402 4.1 72.3 1.0 O A:HOH743 4.1 50.5 1.0 CZ2 A:TRP316 4.1 61.6 1.0 C03 A:OG7603 4.4 78.2 1.0 CB A:CYS402 4.5 64.8 1.0 O4' A:UFP602 4.6 68.1 1.0 CE2 A:TYR342 4.6 66.6 1.0 CD2 A:LEU399 4.7 65.2 1.0 C1' A:UFP602 4.7 60.2 1.0 CZ A:TYR342 4.7 60.8 1.0 O01 A:OG7603 4.8 81.8 1.0 N01 A:OG7603 4.9 72.7 1.0 C08 A:OG7603 4.9 61.8 1.0 CZ3 A:TRP316 5.0 51.3 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 2-(4-((2-Amino-4-Oxo-4,7-Dihydro-3H-Pyrrolo[2, 3-D]Pyrimidin-5-Yl)Methyl)Benzamido)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)Benzoic Acid within 5.0Å range: probe atom residue distance (Å) B Occ B:F602 b:0.8 occ:1.00 F5 B:UFP602 0.0 0.8 1.0 C5 B:UFP602 1.4 99.3 1.0 C6 B:UFP602 2.3 98.5 1.0 C4 B:UFP602 2.4 92.2 1.0 O4 B:UFP602 2.7 89.6 1.0 C05 B:OG7603 3.3 95.5 1.0 C06 B:OG7603 3.4 94.2 1.0 C07 B:OG7603 3.5 91.8 1.0 N1 B:UFP602 3.6 93.1 1.0 N3 B:UFP602 3.6 84.3 1.0 C02 B:OG7603 3.9 0.1 1.0 OH B:TYR342 3.9 69.0 1.0 N03 B:OG7603 4.0 94.2 1.0 C2 B:UFP602 4.1 82.8 1.0 SG B:CYS402 4.1 84.9 1.0 C01 B:OG7603 4.2 91.2 1.0 O B:HOH718 4.3 60.2 1.0 CB B:CYS402 4.4 61.5 1.0 CZ2 B:TRP316 4.4 100.0 1.0 CH2 B:TRP316 4.4 82.6 1.0 CE2 B:TYR342 4.6 64.7 1.0 CZ B:TYR342 4.7 64.5 1.0 C03 B:OG7603 4.7 93.3 1.0 O4' B:UFP602 4.7 81.5 1.0 C1' B:UFP602 4.8 82.0 1.0 CD2 B:LEU399 4.8 89.1 1.0 O01 B:OG7603 5.0 90.7 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)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)Benzoic Acid within 5.0Å range: probe atom residue distance (Å) B Occ C:F602 b:61.3 occ:1.00 F5 C:UFP602 0.0 61.3 1.0 C5 C:UFP602 1.4 84.0 1.0 C6 C:UFP602 2.3 87.6 1.0 C4 C:UFP602 2.4 83.0 1.0 O4 C:UFP602 2.7 84.9 1.0 C05 C:OG7603 3.0 76.1 1.0 C06 C:OG7603 3.1 85.0 1.0 C07 C:OG7603 3.5 77.4 1.0 C02 C:OG7603 3.5 85.4 1.0 N03 C:OG7603 3.6 85.5 1.0 N1 C:UFP602 3.6 84.7 1.0 N3 C:UFP602 3.6 87.7 1.0 C01 C:OG7603 3.8 84.0 1.0 SG C:CYS402 4.1 78.2 1.0 CH2 C:TRP316 4.1 62.1 1.0 C2 C:UFP602 4.1 83.2 1.0 OH C:TYR342 4.1 74.7 1.0 CZ2 C:TRP316 4.2 74.6 1.0 C03 C:OG7603 4.4 88.0 1.0 CD2 C:LEU399 4.5 76.0 1.0 O C:HOH720 4.6 68.8 1.0 O4' C:UFP602 4.6 80.4 1.0 CB C:CYS402 4.6 64.2 1.0 CE2 C:TYR342 4.7 70.3 1.0 O01 C:OG7603 4.7 84.7 1.0 C1' C:UFP602 4.7 68.4 1.0 N01 C:OG7603 4.7 96.9 1.0 CZ C:TYR342 4.8 69.9 1.0 C08 C:OG7603 4.9 69.1 1.0 CZ3 C:TRP316 4.9 62.4 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)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)Benzoic Acid within 5.0Å range: probe atom residue distance (Å) B Occ D:F602 b:0.5 occ:1.00 F5 D:UFP602 0.0 0.5 1.0 C5 D:UFP602 1.4 0.7 1.0 C6 D:UFP602 2.3 0.5 1.0 C4 D:UFP602 2.4 0.3 1.0 O4 D:UFP602 2.7 95.7 1.0 C06 D:OG7603 3.3 0.2 1.0 C05 D:OG7603 3.3 0.7 1.0 N1 D:UFP602 3.6 0.8 1.0 N3 D:UFP602 3.6 94.0 1.0 C07 D:OG7603 3.7 96.8 1.0 N03 D:OG7603 3.8 0.9 1.0 C02 D:OG7603 3.8 0.2 1.0 OH D:TYR342 3.9 74.8 1.0 C01 D:OG7603 4.1 0.3 1.0 C2 D:UFP602 4.1 90.7 1.0 CH2 D:TRP316 4.2 86.5 1.0 CZ2 D:TRP316 4.2 97.1 1.0 SG D:CYS402 4.3 99.9 1.0 CE2 D:TYR342 4.5 76.3 1.0 CB D:CYS402 4.5 73.9 1.0 CZ D:TYR342 4.6 65.3 1.0 O4' D:UFP602 4.6 88.9 1.0 CD2 D:LEU399 4.7 94.6 1.0 C03 D:OG7603 4.7 1.0 1.0 C1' D:UFP602 4.7 93.2 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 2-(4-((2-Amino-4-Oxo-4,7-Dihydro-3H-Pyrrolo[2, 3-D]Pyrimidin-5-Yl)Methyl)Benzamido)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)Benzoic Acid within 5.0Å range: probe atom residue distance (Å) B Occ E:F602 b:0.7 occ:1.00 F5 E:UFP602 0.0 0.7 1.0 C5 E:UFP602 1.4 0.9 1.0 C6 E:UFP602 2.3 0.2 1.0 C4 E:UFP602 2.4 0.2 1.0 O4 E:UFP602 2.7 0.1 1.0 C06 E:OG7603 3.0 0.2 1.0 C05 E:OG7603 3.2 0.4 1.0 N03 E:OG7603 3.4 0.9 1.0 N1 E:UFP602 3.6 1.0 1.0 N3 E:UFP602 3.6 0.3 1.0 C02 E:OG7603 3.7 0.6 1.0 C01 E:OG7603 3.8 0.1 1.0 C07 E:OG7603 3.8 0.7 1.0 OH E:TYR342 4.0 0.6 1.0 SG E:CYS402 4.1 0.6 1.0 C2 E:UFP602 4.1 0.0 1.0 CH2 E:TRP316 4.3 0.8 1.0 CZ2 E:TRP316 4.4 0.1 1.0 CB E:CYS402 4.5 0.3 1.0 CD2 E:LEU399 4.5 0.7 1.0 O4' E:UFP602 4.6 0.4 1.0 C03 E:OG7603 4.7 0.3 1.0 N01 E:OG7603 4.7 0.0 1.0 C1' E:UFP602 4.7 1.0 1.0 CZ E:TYR342 4.8 0.9 1.0 CE2 E:TYR342 4.9 0.6 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