Fluorine in PDB 6ojs: Crystal Structure of Ts-Dhfr From Cryptosporidium Hominis in Complex with Nadph, Fdump, Mtx and 2-Amino-4-Oxo-4,7-Dihydro-Pyrrolo[2,3- D]Pyrimidine-Methyl-Phenyl-D-Glutamic Acid

The structure of Crystal Structure of Ts-Dhfr From Cryptosporidium Hominis in Complex with Nadph, Fdump, Mtx and 2-Amino-4-Oxo-4,7-Dihydro-Pyrrolo[2,3- D]Pyrimidine-Methyl-Phenyl-D-Glutamic Acid, PDB code: 6ojs was solved by D.J.Czyzyk, K.S.Anderson, W.L.Jorgensen, M.Valhondo, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	50.12 / 3.21
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	212.622, 116.188, 220.884, 90.00, 95.48, 90.00
R / Rfree (%)	21.8 / 23.2

The binding sites of Fluorine atom in the Crystal Structure of Ts-Dhfr From Cryptosporidium Hominis in Complex with Nadph, Fdump, Mtx and 2-Amino-4-Oxo-4,7-Dihydro-Pyrrolo[2,3- D]Pyrimidine-Methyl-Phenyl-D-Glutamic Acid (pdb code 6ojs). 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, Mtx and 2-Amino-4-Oxo-4,7-Dihydro-Pyrrolo[2,3- D]Pyrimidine-Methyl-Phenyl-D-Glutamic Acid, PDB code: 6ojs:
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, Mtx and 2-Amino-4-Oxo-4,7-Dihydro-Pyrrolo[2,3- D]Pyrimidine-Methyl-Phenyl-D-Glutamic 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, Mtx and 2-Amino-4-Oxo-4,7-Dihydro-Pyrrolo[2,3- D]Pyrimidine-Methyl-Phenyl-D-Glutamic Acid within 5.0Å range: probe atom residue distance (Å) B Occ A:F602 b:0.1 occ:1.00 F5 A:UFP602 0.0 0.1 1.0 C5 A:UFP602 1.4 0.4 1.0 C6 A:UFP602 2.3 92.3 1.0 C4 A:UFP602 2.4 99.1 1.0 O4 A:UFP602 2.7 0.4 1.0 C6 A:D96603 3.0 95.4 1.0 C5 A:D96603 3.2 97.5 1.0 C7 A:D96603 3.5 97.8 1.0 CZ2 A:TRP316 3.5 0.1 1.0 N1 A:UFP602 3.6 90.7 1.0 N3 A:UFP602 3.6 95.7 1.0 N3 A:D96603 3.7 95.7 1.0 CH2 A:TRP316 3.8 92.0 1.0 C2 A:D96603 3.9 95.7 1.0 OH A:TYR342 4.1 0.6 1.0 C2 A:UFP602 4.1 93.8 1.0 C1 A:D96603 4.2 96.8 1.0 SG A:CYS402 4.3 91.3 1.0 CE2 A:TRP316 4.4 0.8 1.0 OE2 A:GLU294 4.6 89.2 1.0 CE2 A:TYR342 4.6 92.0 1.0 O4' A:UFP602 4.6 90.8 1.0 CZ A:TYR342 4.7 90.9 1.0 C1' A:UFP602 4.7 85.8 1.0 CZ3 A:TRP316 4.9 94.7 1.0 C3 A:D96603 4.9 96.0 1.0 CB A:CYS402 4.9 87.9 1.0 NE1 A:TRP316 4.9 0.8 1.0 C8 A:D96603 5.0 95.9 1.0

Fluorine binding site 2 out of 5 in the Crystal Structure of Ts-Dhfr From Cryptosporidium Hominis in Complex with Nadph, Fdump, Mtx and 2-Amino-4-Oxo-4,7-Dihydro-Pyrrolo[2,3- D]Pyrimidine-Methyl-Phenyl-D-Glutamic 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, Mtx and 2-Amino-4-Oxo-4,7-Dihydro-Pyrrolo[2,3- D]Pyrimidine-Methyl-Phenyl-D-Glutamic Acid within 5.0Å range: probe atom residue distance (Å) B Occ B:F602 b:0.1 occ:1.00 F5 B:UFP602 0.0 0.1 1.0 C5 B:UFP602 1.4 0.6 1.0 C6 B:UFP602 2.3 92.9 1.0 C4 B:UFP602 2.4 0.9 1.0 O4 B:UFP602 2.7 0.7 1.0 C6 B:D96603 3.1 94.0 1.0 C5 B:D96603 3.1 97.0 1.0 C7 B:D96603 3.4 0.9 1.0 CZ2 B:TRP316 3.5 99.5 1.0 N1 B:UFP602 3.6 90.8 1.0 N3 B:UFP602 3.6 0.5 1.0 N3 B:D96603 3.7 96.0 1.0 C2 B:D96603 3.8 98.5 1.0 CH2 B:TRP316 3.9 92.3 1.0 C1 B:D96603 4.1 98.5 1.0 C2 B:UFP602 4.1 97.0 1.0 OH B:TYR342 4.2 0.7 1.0 SG B:CYS402 4.3 91.2 1.0 CE2 B:TRP316 4.4 0.4 1.0 OE2 B:GLU294 4.5 90.0 1.0 CE2 B:TYR342 4.6 94.8 1.0 O4' B:UFP602 4.6 96.6 1.0 C1' B:UFP602 4.7 90.2 1.0 CZ B:TYR342 4.7 93.2 1.0 C3 B:D96603 4.7 0.8 1.0 CB B:CYS402 4.9 90.3 1.0 NE1 B:TRP316 4.9 0.7 1.0 CZ3 B:TRP316 4.9 94.9 1.0 C8 B:D96603 4.9 0.5 1.0

Fluorine binding site 3 out of 5 in the Crystal Structure of Ts-Dhfr From Cryptosporidium Hominis in Complex with Nadph, Fdump, Mtx and 2-Amino-4-Oxo-4,7-Dihydro-Pyrrolo[2,3- D]Pyrimidine-Methyl-Phenyl-D-Glutamic 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, Mtx and 2-Amino-4-Oxo-4,7-Dihydro-Pyrrolo[2,3- D]Pyrimidine-Methyl-Phenyl-D-Glutamic Acid within 5.0Å range: probe atom residue distance (Å) B Occ C:F602 b:0.4 occ:1.00 F5 C:UFP602 0.0 0.4 1.0 C5 C:UFP602 1.4 90.3 1.0 C6 C:UFP602 2.3 81.2 1.0 C4 C:UFP602 2.4 88.4 1.0 O4 C:UFP602 2.7 86.0 1.0 C6 C:D96603 3.0 82.7 1.0 C5 C:D96603 3.2 86.9 1.0 N3 C:D96603 3.5 81.9 1.0 N1 C:UFP602 3.6 83.1 1.0 CZ2 C:TRP316 3.6 84.7 1.0 N3 C:UFP602 3.6 86.2 1.0 C7 C:D96603 3.7 86.5 1.0 C2 C:D96603 3.8 87.6 1.0 CH2 C:TRP316 3.8 78.2 1.0 C1 C:D96603 4.0 82.7 1.0 OH C:TYR342 4.0 96.5 1.0 C2 C:UFP602 4.1 84.8 1.0 SG C:CYS402 4.2 91.4 1.0 CE2 C:TRP316 4.5 88.3 1.0 CE2 C:TYR342 4.6 84.3 1.0 CZ C:TYR342 4.6 84.9 1.0 O4' C:UFP602 4.6 90.8 1.0 C1' C:UFP602 4.7 81.7 1.0 CB C:CYS402 4.8 86.5 1.0 OE2 C:GLU294 4.8 77.4 1.0 CD2 C:LEU399 4.8 76.9 1.0 C3 C:D96603 4.8 86.6 1.0 CZ3 C:TRP316 4.8 80.3 1.0 N1 C:D96603 5.0 84.4 1.0

Fluorine binding site 4 out of 5 in the Crystal Structure of Ts-Dhfr From Cryptosporidium Hominis in Complex with Nadph, Fdump, Mtx and 2-Amino-4-Oxo-4,7-Dihydro-Pyrrolo[2,3- D]Pyrimidine-Methyl-Phenyl-D-Glutamic 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, Mtx and 2-Amino-4-Oxo-4,7-Dihydro-Pyrrolo[2,3- D]Pyrimidine-Methyl-Phenyl-D-Glutamic Acid within 5.0Å range: probe atom residue distance (Å) B Occ D:F602 b:0.7 occ:1.00 F5 D:UFP602 0.0 0.7 1.0 C5 D:UFP602 1.4 0.8 1.0 C6 D:UFP602 2.3 0.2 1.0 C4 D:UFP602 2.4 0.1 1.0 O4 D:UFP602 2.7 0.0 1.0 C6 D:D96603 3.0 0.3 1.0 C5 D:D96603 3.3 0.2 1.0 N3 D:D96603 3.6 0.4 1.0 N1 D:UFP602 3.6 0.1 1.0 N3 D:UFP602 3.6 0.9 1.0 C7 D:D96603 3.8 0.1 1.0 CZ2 D:TRP316 3.9 0.1 1.0 OH D:TYR342 3.9 0.8 1.0 CH2 D:TRP316 4.0 0.9 1.0 C2 D:D96603 4.0 0.7 1.0 C2 D:UFP602 4.1 0.5 1.0 SG D:CYS402 4.1 1.0 1.0 C1 D:D96603 4.1 0.5 1.0 CE2 D:TYR342 4.4 0.9 1.0 CZ D:TYR342 4.5 0.8 1.0 O4' D:UFP602 4.6 0.5 1.0 CB D:CYS402 4.7 0.6 1.0 OE2 D:GLU294 4.7 0.5 1.0 C1' D:UFP602 4.7 0.5 1.0 CE2 D:TRP316 4.9 0.6 1.0 CD2 D:LEU399 4.9 0.9 1.0 NE2 D:HIS403 5.0 0.5 1.0

Fluorine binding site 5 out of 5 in the Crystal Structure of Ts-Dhfr From Cryptosporidium Hominis in Complex with Nadph, Fdump, Mtx and 2-Amino-4-Oxo-4,7-Dihydro-Pyrrolo[2,3- D]Pyrimidine-Methyl-Phenyl-D-Glutamic 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, Mtx and 2-Amino-4-Oxo-4,7-Dihydro-Pyrrolo[2,3- D]Pyrimidine-Methyl-Phenyl-D-Glutamic Acid within 5.0Å range: probe atom residue distance (Å) B Occ E:F602 b:0.9 occ:1.00 F5 E:UFP602 0.0 0.9 1.0 C5 E:UFP602 1.4 88.9 1.0 C6 E:UFP602 2.3 81.8 1.0 C4 E:UFP602 2.4 91.2 1.0 O4 E:UFP602 2.7 93.4 1.0 C6 E:D96603 3.0 86.0 1.0 C5 E:D96603 3.0 86.3 1.0 C7 E:D96603 3.3 90.9 1.0 N1 E:UFP602 3.6 82.0 1.0 N3 E:UFP602 3.6 86.7 1.0 CZ2 E:TRP316 3.6 87.4 1.0 N3 E:D96603 3.7 84.9 1.0 C2 E:D96603 3.7 88.3 1.0 CH2 E:TRP316 3.8 85.4 1.0 OH E:TYR342 3.9 0.4 1.0 SG E:CYS402 4.1 90.1 1.0 C1 E:D96603 4.1 91.0 1.0 C2 E:UFP602 4.1 84.4 1.0 CE2 E:TRP316 4.5 86.6 1.0 CE2 E:TYR342 4.5 96.2 1.0 CZ E:TYR342 4.6 92.1 1.0 O4' E:UFP602 4.6 90.0 1.0 CB E:CYS402 4.7 85.3 1.0 C3 E:D96603 4.7 92.5 1.0 C1' E:UFP602 4.7 83.5 1.0 CZ3 E:TRP316 4.7 87.8 1.0 C8 E:D96603 4.8 89.0 1.0 OE2 E:GLU294 4.9 81.9 1.0 CD2 E:LEU399 4.9 82.4 1.0

D.J.Czyzyk, M.Valhondo, W.L.Jorgensen, K.S.Anderson. Understanding the Structural Basis of Species Selective, Stereospecific Inhibition For Cryptosporidium and Human Thymidylate Synthase. Febs Lett. V. 593 2069 2019.
ISSN: ISSN 0014-5793
PubMed: 31172516
DOI: 10.1002/1873-3468.13474