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

The structure of Crystal Structure of Ts-Dhfr From Cryptosporidium Hominis in Complex with Nadph, Fdump and 2-(2-(4-((2-Amino-4-Oxo-4,7-Dihydro-3H- Pyrrolo[2,3-D]Pyrimidin-5-Yl)Methyl)Benzamido)-4-Methoxyphenyl)Acetic Acid, PDB code: 6pfc 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)	49.56 / 2.69
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	214.982, 117.116, 221.798, 90.00, 95.26, 90.00
R / Rfree (%)	21.3 / 24

The binding sites of Fluorine atom in the Crystal Structure of Ts-Dhfr From Cryptosporidium Hominis in Complex with Nadph, Fdump and 2-(2-(4-((2-Amino-4-Oxo-4,7-Dihydro-3H- Pyrrolo[2,3-D]Pyrimidin-5-Yl)Methyl)Benzamido)-4-Methoxyphenyl)Acetic Acid (pdb code 6pfc). 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-(2-(4-((2-Amino-4-Oxo-4,7-Dihydro-3H- Pyrrolo[2,3-D]Pyrimidin-5-Yl)Methyl)Benzamido)-4-Methoxyphenyl)Acetic Acid, PDB code: 6pfc:
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-(2-(4-((2-Amino-4-Oxo-4,7-Dihydro-3H- Pyrrolo[2,3-D]Pyrimidin-5-Yl)Methyl)Benzamido)-4-Methoxyphenyl)Acetic 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-(2-(4-((2-Amino-4-Oxo-4,7-Dihydro-3H- Pyrrolo[2,3-D]Pyrimidin-5-Yl)Methyl)Benzamido)-4-Methoxyphenyl)Acetic Acid within 5.0Å range: probe atom residue distance (Å) B Occ A:F602 b:91.6 occ:1.00 F5 A:UFP602 0.0 91.6 1.0 C5 A:UFP602 1.4 84.0 1.0 C6 A:UFP602 2.3 83.9 1.0 C4 A:UFP602 2.4 85.7 1.0 O4 A:UFP602 2.7 85.9 1.0 C5 A:OED603 3.2 97.7 1.0 C6 A:OED603 3.3 93.6 1.0 C7 A:OED603 3.5 99.8 1.0 N1 A:UFP602 3.6 79.1 1.0 N3 A:UFP602 3.6 84.5 1.0 C2 A:OED603 3.8 97.2 1.0 N3 A:OED603 3.9 93.4 1.0 OH A:TYR342 4.1 84.2 1.0 C2 A:UFP602 4.1 73.9 1.0 SG A:CYS402 4.1 92.9 1.0 C1 A:OED603 4.2 92.5 1.0 CH2 A:TRP316 4.2 90.1 1.0 CZ2 A:TRP316 4.2 0.5 1.0 CB A:CYS402 4.5 71.1 1.0 O4' A:UFP602 4.6 92.2 1.0 CE2 A:TYR342 4.6 89.3 1.0 CD2 A:LEU399 4.7 94.8 1.0 C3 A:OED603 4.7 93.4 1.0 C1' A:UFP602 4.7 87.3 1.0 CZ A:TYR342 4.8 83.7 1.0 C8 A:OED603 5.0 93.7 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-(2-(4-((2-Amino-4-Oxo-4,7-Dihydro-3H- Pyrrolo[2,3-D]Pyrimidin-5-Yl)Methyl)Benzamido)-4-Methoxyphenyl)Acetic 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-(2-(4-((2-Amino-4-Oxo-4,7-Dihydro-3H- Pyrrolo[2,3-D]Pyrimidin-5-Yl)Methyl)Benzamido)-4-Methoxyphenyl)Acetic Acid within 5.0Å range: probe atom residue distance (Å) B Occ B:F602 b:80.4 occ:1.00 F5 B:UFP602 0.0 80.4 1.0 C5 B:UFP602 1.4 77.0 1.0 C6 B:UFP602 2.3 73.3 1.0 C4 B:UFP602 2.4 73.4 1.0 O4 B:UFP602 2.7 67.5 1.0 C5 B:OED603 3.2 77.7 1.0 C6 B:OED603 3.4 78.4 1.0 C7 B:OED603 3.5 68.4 1.0 N1 B:UFP602 3.6 67.4 1.0 N3 B:UFP602 3.6 70.8 1.0 C2 B:OED603 3.8 81.9 1.0 N3 B:OED603 3.9 72.3 1.0 C2 B:UFP602 4.1 65.7 1.0 SG B:CYS402 4.1 71.6 1.0 C1 B:OED603 4.2 75.0 1.0 CZ2 B:TRP316 4.2 65.5 1.0 CH2 B:TRP316 4.2 70.7 1.0 OH B:TYR342 4.2 70.6 1.0 O B:HOH743 4.4 59.7 1.0 CB B:CYS402 4.5 58.6 1.0 O4' B:UFP602 4.6 69.3 1.0 C3 B:OED603 4.6 74.2 1.0 CE2 B:TYR342 4.7 54.3 1.0 C1' B:UFP602 4.7 66.2 1.0 CD2 B:LEU399 4.8 75.2 1.0 CZ B:TYR342 4.9 49.7 1.0 O1 B:OED603 4.9 69.0 1.0 C8 B:OED603 4.9 69.6 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-(2-(4-((2-Amino-4-Oxo-4,7-Dihydro-3H- Pyrrolo[2,3-D]Pyrimidin-5-Yl)Methyl)Benzamido)-4-Methoxyphenyl)Acetic 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-(2-(4-((2-Amino-4-Oxo-4,7-Dihydro-3H- Pyrrolo[2,3-D]Pyrimidin-5-Yl)Methyl)Benzamido)-4-Methoxyphenyl)Acetic Acid within 5.0Å range: probe atom residue distance (Å) B Occ C:F602 b:77.4 occ:1.00 F5 C:UFP602 0.0 77.4 1.0 C5 C:UFP602 1.4 77.1 1.0 C6 C:UFP602 2.3 71.8 1.0 C4 C:UFP602 2.4 68.1 1.0 O4 C:UFP602 2.8 65.3 1.0 C5 C:OED603 3.1 71.7 1.0 C6 C:OED603 3.2 69.5 1.0 C7 C:OED603 3.4 65.6 1.0 N1 C:UFP602 3.6 65.4 1.0 N3 C:UFP602 3.6 61.9 1.0 C2 C:OED603 3.7 77.4 1.0 N3 C:OED603 3.8 70.0 1.0 C1 C:OED603 4.1 62.3 1.0 C2 C:UFP602 4.1 64.5 1.0 SG C:CYS402 4.2 67.7 1.0 OH C:TYR342 4.2 69.1 1.0 CH2 C:TRP316 4.4 58.1 1.0 CZ2 C:TRP316 4.4 69.2 1.0 CB C:CYS402 4.6 62.1 1.0 C3 C:OED603 4.6 71.3 1.0 O4' C:UFP602 4.6 65.7 1.0 CD2 C:LEU399 4.6 67.1 1.0 CE2 C:TYR342 4.6 61.0 1.0 C1' C:UFP602 4.7 61.6 1.0 CZ C:TYR342 4.8 52.8 1.0 C8 C:OED603 4.9 60.1 1.0 O1 C:OED603 4.9 75.0 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-(2-(4-((2-Amino-4-Oxo-4,7-Dihydro-3H- Pyrrolo[2,3-D]Pyrimidin-5-Yl)Methyl)Benzamido)-4-Methoxyphenyl)Acetic 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-(2-(4-((2-Amino-4-Oxo-4,7-Dihydro-3H- Pyrrolo[2,3-D]Pyrimidin-5-Yl)Methyl)Benzamido)-4-Methoxyphenyl)Acetic Acid within 5.0Å range: probe atom residue distance (Å) B Occ D:F602 b:73.7 occ:1.00 F5 D:UFP602 0.0 73.7 1.0 C5 D:UFP602 1.4 64.4 1.0 C6 D:UFP602 2.3 60.5 1.0 C4 D:UFP602 2.4 59.4 1.0 O4 D:UFP602 2.7 63.6 1.0 C5 D:OED603 3.1 60.5 1.0 C6 D:OED603 3.2 64.2 1.0 C7 D:OED603 3.4 65.7 1.0 N1 D:UFP602 3.6 59.1 1.0 N3 D:UFP602 3.6 65.7 1.0 O D:HOH738 3.7 44.8 1.0 C2 D:OED603 3.7 64.3 1.0 N3 D:OED603 3.8 65.8 1.0 C2 D:UFP602 4.1 62.5 1.0 C1 D:OED603 4.1 59.6 1.0 CZ2 D:TRP316 4.2 53.2 1.0 OH D:TYR342 4.2 62.0 1.0 SG D:CYS402 4.2 65.1 1.0 CH2 D:TRP316 4.2 54.5 1.0 O D:HOH757 4.3 47.0 1.0 CB D:CYS402 4.5 55.8 1.0 CD2 D:LEU399 4.6 56.8 1.0 O4' D:UFP602 4.6 57.4 1.0 C3 D:OED603 4.6 66.5 1.0 CE2 D:TYR342 4.6 53.8 1.0 C1' D:UFP602 4.7 54.9 1.0 CZ D:TYR342 4.8 54.5 1.0 C8 D:OED603 4.8 59.0 1.0 O1 D:OED603 4.9 65.2 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-(2-(4-((2-Amino-4-Oxo-4,7-Dihydro-3H- Pyrrolo[2,3-D]Pyrimidin-5-Yl)Methyl)Benzamido)-4-Methoxyphenyl)Acetic 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-(2-(4-((2-Amino-4-Oxo-4,7-Dihydro-3H- Pyrrolo[2,3-D]Pyrimidin-5-Yl)Methyl)Benzamido)-4-Methoxyphenyl)Acetic Acid within 5.0Å range: probe atom residue distance (Å) B Occ E:F602 b:69.0 occ:1.00 F5 E:UFP602 0.0 69.0 1.0 C5 E:UFP602 1.4 63.2 1.0 C6 E:UFP602 2.3 57.6 1.0 C4 E:UFP602 2.4 59.5 1.0 O4 E:UFP602 2.7 60.2 1.0 C5 E:OED603 3.2 56.6 1.0 C6 E:OED603 3.2 56.9 1.0 C7 E:OED603 3.5 67.0 1.0 O E:HOH730 3.5 44.2 1.0 N1 E:UFP602 3.6 50.5 1.0 N3 E:UFP602 3.6 62.9 1.0 C2 E:OED603 3.7 64.5 1.0 N3 E:OED603 3.8 60.5 1.0 C1 E:OED603 4.1 56.3 1.0 C2 E:UFP602 4.1 54.6 1.0 SG E:CYS402 4.1 56.3 1.0 OH E:TYR342 4.1 56.5 1.0 CH2 E:TRP316 4.1 51.0 1.0 CZ2 E:TRP316 4.2 50.2 1.0 O E:HOH783 4.4 50.8 1.0 CB E:CYS402 4.4 52.1 1.0 CE2 E:TYR342 4.6 50.0 1.0 C3 E:OED603 4.6 64.4 1.0 O4' E:UFP602 4.7 51.1 1.0 C1' E:UFP602 4.7 48.4 1.0 CD2 E:LEU399 4.8 57.2 1.0 CZ E:TYR342 4.8 51.9 1.0 O1 E:OED603 4.9 65.7 1.0 C8 E:OED603 5.0 54.7 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