Fluorine in PDB 6pff: 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-Cyanobenzoic 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-Cyanobenzoic Acid., PDB code: 6pff 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)	48.82 / 2.98
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	213.424, 116.794, 221.760, 90.00, 95.69, 90.00
R / Rfree (%)	20.9 / 23.9

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-Cyanobenzoic Acid. (pdb code 6pff). 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-Cyanobenzoic Acid., PDB code: 6pff:
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-Cyanobenzoic 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-Cyanobenzoic Acid. within 5.0Å range: probe atom residue distance (Å) B Occ A:F602 b:90.7 occ:1.00 F5 A:UFP602 0.0 90.7 1.0 C5 A:UFP602 1.4 82.9 1.0 C6 A:UFP602 2.3 76.4 1.0 C4 A:UFP602 2.4 79.0 1.0 O4 A:UFP602 2.7 65.8 1.0 C6 A:OG1603 3.6 82.7 1.0 C5 A:OG1603 3.6 86.0 1.0 N1 A:UFP602 3.6 78.2 1.0 N3 A:UFP602 3.6 81.6 1.0 OH A:TYR342 3.7 55.2 1.0 SG A:CYS402 3.9 70.7 1.0 C7 A:OG1603 3.9 76.1 1.0 CB A:CYS402 4.0 59.7 1.0 N3 A:OG1603 4.0 95.8 1.0 C2 A:OG1603 4.1 89.7 1.0 C2 A:UFP602 4.1 74.3 1.0 CE2 A:TYR342 4.3 52.5 1.0 C1 A:OG1603 4.3 89.9 1.0 CZ A:TYR342 4.4 50.4 1.0 CH2 A:TRP316 4.6 73.0 1.0 O4' A:UFP602 4.6 77.2 1.0 CZ2 A:TRP316 4.6 79.7 1.0 CD2 A:HIS403 4.7 57.4 1.0 C1' A:UFP602 4.7 76.9 1.0 NE2 A:HIS403 4.9 57.4 1.0 C3 A:OG1603 4.9 81.9 1.0 CD2 A:LEU399 4.9 81.3 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)-4-Cyanobenzoic 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-Cyanobenzoic Acid. within 5.0Å range: probe atom residue distance (Å) B Occ B:F602 b:75.2 occ:1.00 F5 B:UFP602 0.0 75.2 1.0 C5 B:UFP602 1.4 62.3 1.0 C6 B:UFP602 2.3 61.0 1.0 C4 B:UFP602 2.4 63.3 1.0 O4 B:UFP602 2.7 51.8 1.0 C5 B:OG1603 3.2 63.9 1.0 C6 B:OG1603 3.3 64.7 1.0 C7 B:OG1603 3.5 52.3 1.0 N1 B:UFP602 3.6 60.6 1.0 N3 B:UFP602 3.6 74.3 1.0 C2 B:OG1603 3.8 71.6 1.0 OH B:TYR342 3.9 57.8 1.0 N3 B:OG1603 3.9 77.9 1.0 C2 B:UFP602 4.1 60.4 1.0 SG B:CYS402 4.2 69.6 1.0 C1 B:OG1603 4.2 64.8 1.0 CZ2 B:TRP316 4.2 53.7 1.0 CH2 B:TRP316 4.2 49.3 1.0 CE2 B:TYR342 4.3 47.0 1.0 CB B:CYS402 4.3 47.8 1.0 CZ B:TYR342 4.5 49.4 1.0 O4' B:UFP602 4.6 63.7 1.0 C3 B:OG1603 4.7 66.3 1.0 C1' B:UFP602 4.7 55.6 1.0 CD2 B:LEU399 4.8 58.6 1.0 CD2 B:HIS403 4.9 47.9 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-Cyanobenzoic 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-Cyanobenzoic Acid. within 5.0Å range: probe atom residue distance (Å) B Occ C:F602 b:0.3 occ:1.00 F5 C:UFP602 0.0 0.3 1.0 C5 C:UFP602 1.4 0.0 1.0 C6 C:UFP602 2.3 89.8 1.0 C4 C:UFP602 2.4 94.3 1.0 O4 C:UFP602 2.7 78.8 1.0 C5 C:OG1603 3.2 0.4 1.0 C6 C:OG1603 3.3 97.2 1.0 C7 C:OG1603 3.5 90.9 1.0 N1 C:UFP602 3.6 90.2 1.0 N3 C:UFP602 3.6 91.1 1.0 C2 C:OG1603 3.8 1.0 1.0 N3 C:OG1603 3.8 0.6 1.0 OH C:TYR342 4.1 77.6 1.0 CZ2 C:TRP316 4.1 82.6 1.0 C2 C:UFP602 4.1 82.8 1.0 C1 C:OG1603 4.1 0.4 1.0 SG C:CYS402 4.1 78.2 1.0 CH2 C:TRP316 4.1 84.4 1.0 CE2 C:TYR342 4.3 71.8 1.0 CB C:CYS402 4.5 71.8 1.0 CZ C:TYR342 4.6 67.3 1.0 O4' C:UFP602 4.6 0.4 1.0 C3 C:OG1603 4.7 0.4 1.0 C1' C:UFP602 4.7 91.0 1.0 CD2 C:LEU399 4.9 87.0 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-(4-((2-Amino-4-Oxo-4,7-Dihydro-3H-Pyrrolo[2, 3-D]Pyrimidin-5-Yl)Methyl)Benzamido)-4-Cyanobenzoic 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-Cyanobenzoic Acid. within 5.0Å range: probe atom residue distance (Å) B Occ D:F602 b:81.8 occ:1.00 F5 D:UFP602 0.0 81.8 1.0 C5 D:UFP602 1.4 67.9 1.0 C6 D:UFP602 2.3 65.5 1.0 C4 D:UFP602 2.4 71.3 1.0 O4 D:UFP602 2.7 59.6 1.0 C5 D:OG1603 3.1 68.8 1.0 C6 D:OG1603 3.2 68.8 1.0 C7 D:OG1603 3.4 66.5 1.0 N1 D:UFP602 3.6 71.7 1.0 N3 D:UFP602 3.6 75.6 1.0 C2 D:OG1603 3.7 77.5 1.0 N3 D:OG1603 3.8 89.4 1.0 OH D:TYR342 3.9 63.6 1.0 C1 D:OG1603 4.1 83.6 1.0 C2 D:UFP602 4.1 69.0 1.0 SG D:CYS402 4.1 68.8 1.0 CH2 D:TRP316 4.2 59.8 1.0 CZ2 D:TRP316 4.2 51.8 1.0 CE2 D:TYR342 4.3 58.7 1.0 CB D:CYS402 4.4 58.8 1.0 CZ D:TYR342 4.5 58.0 1.0 O4' D:UFP602 4.6 67.0 1.0 C3 D:OG1603 4.6 76.1 1.0 CD2 D:LEU399 4.6 57.8 1.0 C1' D:UFP602 4.7 61.7 1.0 C8 D:OG1603 4.9 66.4 1.0 O1 D:OG1603 5.0 80.9 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-Cyanobenzoic 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-Cyanobenzoic Acid. within 5.0Å range: probe atom residue distance (Å) B Occ E:F602 b:0.0 occ:1.00 F5 E:UFP602 0.0 0.0 1.0 C5 E:UFP602 1.4 0.5 1.0 C6 E:UFP602 2.3 0.9 1.0 C4 E:UFP602 2.4 0.7 1.0 O4 E:UFP602 2.7 0.0 1.0 C6 E:OG1603 3.4 0.8 1.0 C5 E:OG1603 3.5 0.9 1.0 N1 E:UFP602 3.6 0.2 1.0 N3 E:UFP602 3.6 0.2 1.0 OH E:TYR342 3.7 0.5 1.0 C7 E:OG1603 3.8 0.8 1.0 N3 E:OG1603 4.0 0.5 1.0 CH2 E:TRP316 4.1 0.5 1.0 SG E:CYS402 4.1 0.9 1.0 C2 E:UFP602 4.1 0.5 1.0 C2 E:OG1603 4.1 0.7 1.0 CE2 E:TYR342 4.1 0.0 1.0 CZ2 E:TRP316 4.2 0.2 1.0 CB E:CYS402 4.3 89.3 1.0 CZ E:TYR342 4.3 98.4 1.0 C1 E:OG1603 4.4 0.1 1.0 CD2 E:LEU399 4.5 0.1 1.0 O4' E:UFP602 4.6 0.5 1.0 C1' E:UFP602 4.7 0.5 1.0 CD2 E:HIS403 5.0 0.7 1.0 CZ3 E:TRP316 5.0 0.7 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