Fluorine in PDB 6pfe: 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-Methoxybenzoic 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-Methoxybenzoic Acid., PDB code: 6pfe 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)	49.44 / 2.81
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	212.859, 115.641, 219.899, 90.00, 95.00, 90.00
R / Rfree (%)	22.7 / 25.7

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-Methoxybenzoic Acid. (pdb code 6pfe). 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-Methoxybenzoic Acid., PDB code: 6pfe:
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-Methoxybenzoic 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-Methoxybenzoic Acid. within 5.0Å range: probe atom residue distance (Å) B Occ A:F602 b:55.1 occ:1.00 F5 A:UFP602 0.0 55.1 1.0 C5 A:UFP602 1.4 69.7 1.0 C6 A:UFP602 2.3 72.6 1.0 C4 A:UFP602 2.4 69.6 1.0 O4 A:UFP602 2.8 69.4 1.0 C5 A:OEA603 2.9 67.8 1.0 C6 A:OEA603 3.0 67.8 1.0 C7 A:OEA603 3.4 66.0 1.0 C3 A:OEA603 3.4 77.5 1.0 N3 A:OEA603 3.4 72.4 1.0 N1 A:UFP602 3.6 63.6 1.0 N3 A:UFP602 3.6 69.8 1.0 C2 A:OEA603 3.7 70.6 1.0 OH A:TYR342 4.0 76.9 1.0 SG A:CYS402 4.0 71.9 1.0 CH2 A:TRP316 4.0 55.9 1.0 CZ2 A:TRP316 4.1 63.6 1.0 C2 A:UFP602 4.1 63.3 1.0 C4 A:OEA603 4.3 73.6 1.0 CD2 A:LEU399 4.5 68.8 1.0 O4' A:UFP602 4.5 66.9 1.0 CB A:CYS402 4.6 59.5 1.0 N2 A:OEA603 4.7 65.6 1.0 C1' A:UFP602 4.7 55.6 1.0 CE2 A:TYR342 4.8 68.0 1.0 CZ A:TYR342 4.8 68.8 1.0 O1 A:OEA603 4.8 75.6 1.0 C8 A:OEA603 4.9 48.5 1.0 CZ3 A:TRP316 4.9 61.4 1.0 CE2 A:TRP316 5.0 60.7 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-(4-((2-Amino-4-Oxo-4,7-Dihydro-3H-Pyrrolo[2, 3-D]Pyrimidin-5-Yl)Methyl)Benzamido)-4-Methoxybenzoic 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-Methoxybenzoic Acid. within 5.0Å range: probe atom residue distance (Å) B Occ B:F602 b:85.5 occ:1.00 F5 B:UFP602 0.0 85.5 1.0 C5 B:UFP602 1.4 80.0 1.0 C6 B:UFP602 2.3 85.4 1.0 C4 B:UFP602 2.4 87.7 1.0 O4 B:UFP602 2.7 96.6 1.0 C5 B:OEA603 3.0 77.8 1.0 C6 B:OEA603 3.2 75.7 1.0 C7 B:OEA603 3.3 75.7 1.0 C3 B:OEA603 3.5 83.7 1.0 N1 B:UFP602 3.6 86.0 1.0 N3 B:UFP602 3.6 84.4 1.0 N3 B:OEA603 3.8 76.7 1.0 CZ2 B:TRP316 3.9 79.1 1.0 OH B:TYR342 3.9 85.4 1.0 C2 B:OEA603 4.0 77.0 1.0 CH2 B:TRP316 4.0 67.3 1.0 SG B:CYS402 4.1 75.3 1.0 C2 B:UFP602 4.1 80.8 1.0 O B:HOH714 4.2 55.5 1.0 C4 B:OEA603 4.3 79.9 1.0 O4' B:UFP602 4.6 65.8 1.0 CB B:CYS402 4.6 73.1 1.0 O1 B:OEA603 4.7 82.7 1.0 CZ B:TYR342 4.7 67.8 1.0 C1' B:UFP602 4.7 71.8 1.0 CE2 B:TYR342 4.7 58.9 1.0 C8 B:OEA603 4.8 75.1 1.0 CE2 B:TRP316 4.8 79.2 1.0 CD2 B:LEU399 4.9 67.6 1.0 N2 B:OEA603 5.0 78.0 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-Methoxybenzoic 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-Methoxybenzoic Acid. within 5.0Å range: probe atom residue distance (Å) B Occ C:F602 b:67.4 occ:1.00 F5 C:UFP602 0.0 67.4 1.0 C5 C:UFP602 1.4 66.5 1.0 C6 C:UFP602 2.3 72.0 1.0 C4 C:UFP602 2.4 67.3 1.0 O4 C:UFP602 2.8 74.4 1.0 C5 C:OEA603 3.0 61.8 1.0 C6 C:OEA603 3.0 69.6 1.0 C7 C:OEA603 3.5 77.2 1.0 N3 C:OEA603 3.6 83.5 1.0 C3 C:OEA603 3.6 88.6 1.0 N1 C:UFP602 3.6 77.2 1.0 N3 C:UFP602 3.6 72.2 1.0 CZ2 C:TRP316 3.8 62.6 1.0 C2 C:OEA603 3.8 80.8 1.0 CH2 C:TRP316 3.9 54.1 1.0 SG C:CYS402 4.0 67.0 1.0 C2 C:UFP602 4.1 72.6 1.0 OH C:TYR342 4.1 73.5 1.0 CD2 C:LEU399 4.3 62.5 1.0 C4 C:OEA603 4.5 87.0 1.0 O4' C:UFP602 4.5 73.8 1.0 CE2 C:TRP316 4.6 56.9 1.0 C1' C:UFP602 4.7 67.4 1.0 CB C:CYS402 4.7 64.8 1.0 CE2 C:TYR342 4.7 65.7 1.0 N2 C:OEA603 4.8 69.0 1.0 CZ C:TYR342 4.9 70.2 1.0 CZ3 C:TRP316 4.9 52.1 1.0 C8 C:OEA603 4.9 79.8 1.0 O1 C:OEA603 5.0 84.3 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-Methoxybenzoic 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-Methoxybenzoic Acid. within 5.0Å range: probe atom residue distance (Å) B Occ D:F602 b:90.5 occ:1.00 F5 D:UFP602 0.0 90.5 1.0 C5 D:UFP602 1.4 90.7 1.0 C6 D:UFP602 2.3 96.1 1.0 C4 D:UFP602 2.4 89.3 1.0 O4 D:UFP602 2.7 84.3 1.0 C6 D:OEA603 3.0 99.0 1.0 C5 D:OEA603 3.1 0.3 1.0 N3 D:OEA603 3.5 95.6 1.0 C3 D:OEA603 3.6 0.8 1.0 N1 D:UFP602 3.6 93.8 1.0 C7 D:OEA603 3.6 93.1 1.0 N3 D:UFP602 3.6 89.7 1.0 C2 D:OEA603 3.8 93.4 1.0 OH D:TYR342 3.9 93.5 1.0 SG D:CYS402 3.9 85.7 1.0 C2 D:UFP602 4.1 83.5 1.0 CZ2 D:TRP316 4.2 97.7 1.0 CH2 D:TRP316 4.2 90.4 1.0 C4 D:OEA603 4.5 97.5 1.0 CD2 D:LEU399 4.6 90.7 1.0 CB D:CYS402 4.6 79.5 1.0 O4' D:UFP602 4.6 93.0 1.0 CZ D:TYR342 4.7 87.7 1.0 CE2 D:TYR342 4.7 92.2 1.0 C1' D:UFP602 4.7 91.2 1.0 N2 D:OEA603 4.8 97.8 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)-4-Methoxybenzoic 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-Methoxybenzoic Acid. within 5.0Å range: probe atom residue distance (Å) B Occ E:F602 b:85.7 occ:1.00 F5 E:UFP602 0.0 85.7 1.0 C5 E:UFP602 1.4 79.9 1.0 C6 E:UFP602 2.3 81.9 1.0 C4 E:UFP602 2.4 77.0 1.0 O4 E:UFP602 2.8 72.7 1.0 C5 E:OEA603 3.1 75.9 1.0 C6 E:OEA603 3.1 74.0 1.0 C3 E:OEA603 3.5 85.7 1.0 N3 E:OEA603 3.5 84.5 1.0 C7 E:OEA603 3.6 74.4 1.0 N1 E:UFP602 3.6 79.2 1.0 N3 E:UFP602 3.6 76.8 1.0 C2 E:OEA603 3.7 79.6 1.0 OH E:TYR342 3.9 80.2 1.0 CZ2 E:TRP316 4.0 78.5 1.0 CH2 E:TRP316 4.1 81.1 1.0 C2 E:UFP602 4.1 77.4 1.0 SG E:CYS402 4.1 75.1 1.0 C4 E:OEA603 4.4 83.4 1.0 CE2 E:TYR342 4.6 77.8 1.0 O4' E:UFP602 4.6 79.0 1.0 CB E:CYS402 4.6 66.3 1.0 N2 E:OEA603 4.6 85.8 1.0 CD2 E:LEU399 4.7 90.9 1.0 CZ E:TYR342 4.7 63.2 1.0 C1' E:UFP602 4.7 75.1 1.0 O1 E:OEA603 4.9 84.7 1.0 CE2 E:TRP316 5.0 76.5 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