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Fluorine in PDB 4ky8: Crystal Structure of Ts-Dhfr From Cryptosporidium Hominis in Complex with Nadph, Methotrexate, Fdump and 4-((2-Amino-6-Methyl-4-Oxo-4,7- Dihydro-3H-Pyrrolo[2,3-D]Pyrimidin-5-Yl)Thio)-2-Chlorophenyl)-L- Glutamic Acid

Enzymatic activity of Crystal Structure of Ts-Dhfr From Cryptosporidium Hominis in Complex with Nadph, Methotrexate, Fdump and 4-((2-Amino-6-Methyl-4-Oxo-4,7- Dihydro-3H-Pyrrolo[2,3-D]Pyrimidin-5-Yl)Thio)-2-Chlorophenyl)-L- Glutamic Acid

All present enzymatic activity of Crystal Structure of Ts-Dhfr From Cryptosporidium Hominis in Complex with Nadph, Methotrexate, Fdump and 4-((2-Amino-6-Methyl-4-Oxo-4,7- Dihydro-3H-Pyrrolo[2,3-D]Pyrimidin-5-Yl)Thio)-2-Chlorophenyl)-L- Glutamic Acid:
1.5.1.3; 2.1.1.45;

Protein crystallography data

The structure of Crystal Structure of Ts-Dhfr From Cryptosporidium Hominis in Complex with Nadph, Methotrexate, Fdump and 4-((2-Amino-6-Methyl-4-Oxo-4,7- Dihydro-3H-Pyrrolo[2,3-D]Pyrimidin-5-Yl)Thio)-2-Chlorophenyl)-L- Glutamic Acid, PDB code: 4ky8 was solved by V.P.Kumar, K.S.Anderson, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 48.12 / 3.08
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 214.162, 115.665, 218.767, 90.00, 94.36, 90.00
R / Rfree (%) 23.2 / 26.6

Other elements in 4ky8:

The structure of Crystal Structure of Ts-Dhfr From Cryptosporidium Hominis in Complex with Nadph, Methotrexate, Fdump and 4-((2-Amino-6-Methyl-4-Oxo-4,7- Dihydro-3H-Pyrrolo[2,3-D]Pyrimidin-5-Yl)Thio)-2-Chlorophenyl)-L- Glutamic Acid also contains other interesting chemical elements:

Chlorine (Cl) 5 atoms

Fluorine Binding Sites:

The binding sites of Fluorine atom in the Crystal Structure of Ts-Dhfr From Cryptosporidium Hominis in Complex with Nadph, Methotrexate, Fdump and 4-((2-Amino-6-Methyl-4-Oxo-4,7- Dihydro-3H-Pyrrolo[2,3-D]Pyrimidin-5-Yl)Thio)-2-Chlorophenyl)-L- Glutamic Acid (pdb code 4ky8). 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, Methotrexate, Fdump and 4-((2-Amino-6-Methyl-4-Oxo-4,7- Dihydro-3H-Pyrrolo[2,3-D]Pyrimidin-5-Yl)Thio)-2-Chlorophenyl)-L- Glutamic Acid, PDB code: 4ky8:
Jump to Fluorine binding site number: 1; 2; 3; 4; 5;

Fluorine binding site 1 out of 5 in 4ky8

Go back to Fluorine Binding Sites List in 4ky8
Fluorine binding site 1 out of 5 in the Crystal Structure of Ts-Dhfr From Cryptosporidium Hominis in Complex with Nadph, Methotrexate, Fdump and 4-((2-Amino-6-Methyl-4-Oxo-4,7- Dihydro-3H-Pyrrolo[2,3-D]Pyrimidin-5-Yl)Thio)-2-Chlorophenyl)-L- 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, Methotrexate, Fdump and 4-((2-Amino-6-Methyl-4-Oxo-4,7- Dihydro-3H-Pyrrolo[2,3-D]Pyrimidin-5-Yl)Thio)-2-Chlorophenyl)-L- Glutamic Acid within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F602

b:0.5
occ:1.00
 F5 A:UFP602 0.0 0.5 1.0
C5 A:UFP602 1.4 88.4 1.0
C6 A:UFP602 2.3 80.7 1.0
C4 A:UFP602 2.4 87.2 1.0
O4 A:UFP602 2.7 84.1 1.0
N1 A:UFP602 3.6 80.3 1.0
N3 A:UFP602 3.6 84.4 1.0
CAX A:1UF604 3.7 82.9 1.0
CAA A:1UF604 3.7 78.2 1.0
CBB A:1UF604 3.8 81.0 1.0
OH A:TYR342 3.9 0.4 1.0
SAS A:1UF604 4.0 85.2 1.0
C2 A:UFP602 4.1 82.5 1.0
CZ2 A:TRP316 4.2 63.4 1.0
SG A:CYS402 4.3 85.2 1.0
CH2 A:TRP316 4.3 60.7 1.0
NAR A:1UF604 4.4 89.2 1.0
CB A:CYS402 4.4 73.3 1.0
CE2 A:TYR342 4.5 0.4 1.0
CBE A:1UF604 4.5 81.8 1.0
CD2 A:LEU399 4.6 66.9 1.0
CZ A:TYR342 4.6 0.3 1.0
O4' A:UFP602 4.7 79.3 1.0
C1' A:UFP602 4.8 80.7 1.0
CD2 A:HIS403 4.8 80.2 1.0
CBD A:1UF604 4.9 82.7 1.0
NE2 A:HIS403 4.9 83.3 1.0

Fluorine binding site 2 out of 5 in 4ky8

Go back to Fluorine Binding Sites List in 4ky8
Fluorine binding site 2 out of 5 in the Crystal Structure of Ts-Dhfr From Cryptosporidium Hominis in Complex with Nadph, Methotrexate, Fdump and 4-((2-Amino-6-Methyl-4-Oxo-4,7- Dihydro-3H-Pyrrolo[2,3-D]Pyrimidin-5-Yl)Thio)-2-Chlorophenyl)-L- 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, Methotrexate, Fdump and 4-((2-Amino-6-Methyl-4-Oxo-4,7- Dihydro-3H-Pyrrolo[2,3-D]Pyrimidin-5-Yl)Thio)-2-Chlorophenyl)-L- Glutamic Acid within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F602

b:0.9
occ:1.00
 F5 B:UFP602 0.0 0.9 1.0
C5 B:UFP602 1.4 91.8 1.0
C6 B:UFP602 2.3 84.2 1.0
C4 B:UFP602 2.4 90.6 1.0
O4 B:UFP602 2.7 87.5 1.0
N1 B:UFP602 3.6 83.8 1.0
N3 B:UFP602 3.6 87.8 1.0
CAA B:1UF604 3.7 87.6 1.0
CAX B:1UF604 3.7 92.2 1.0
OH B:TYR342 3.8 86.9 1.0
CBB B:1UF604 3.8 90.3 1.0
SAS B:1UF604 3.8 94.5 1.0
C2 B:UFP602 4.1 86.0 1.0
SG B:CYS402 4.2 0.1 1.0
CB B:CYS402 4.3 88.3 1.0
CE2 B:TYR342 4.4 83.9 1.0
CZ2 B:TRP316 4.4 94.5 1.0
CZ B:TYR342 4.5 85.8 1.0
CH2 B:TRP316 4.5 91.8 1.0
NAR B:1UF604 4.5 98.5 1.0
CD2 B:HIS403 4.6 76.2 1.0
CBE B:1UF604 4.6 91.2 1.0
CD2 B:LEU399 4.7 71.0 1.0
NE2 B:HIS403 4.7 79.4 1.0
O4' B:UFP602 4.7 82.8 1.0
C1' B:UFP602 4.8 84.2 1.0

Fluorine binding site 3 out of 5 in 4ky8

Go back to Fluorine Binding Sites List in 4ky8
Fluorine binding site 3 out of 5 in the Crystal Structure of Ts-Dhfr From Cryptosporidium Hominis in Complex with Nadph, Methotrexate, Fdump and 4-((2-Amino-6-Methyl-4-Oxo-4,7- Dihydro-3H-Pyrrolo[2,3-D]Pyrimidin-5-Yl)Thio)-2-Chlorophenyl)-L- 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, Methotrexate, Fdump and 4-((2-Amino-6-Methyl-4-Oxo-4,7- Dihydro-3H-Pyrrolo[2,3-D]Pyrimidin-5-Yl)Thio)-2-Chlorophenyl)-L- 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 91.3 1.0
C6 C:UFP602 2.3 83.7 1.0
C4 C:UFP602 2.4 90.1 1.0
O4 C:UFP602 2.7 87.0 1.0
CBB C:1UF604 3.6 88.4 1.0
N1 C:UFP602 3.6 83.3 1.0
SAS C:1UF604 3.6 92.6 1.0
N3 C:UFP602 3.6 87.4 1.0
CAX C:1UF604 3.7 90.3 1.0
CAA C:1UF604 3.7 85.6 1.0
OH C:TYR342 4.1 1.0 1.0
C2 C:UFP602 4.1 85.5 1.0
CZ2 C:TRP316 4.2 66.3 1.0
SG C:CYS402 4.3 0.7 1.0
CH2 C:TRP316 4.4 63.6 1.0
CBE C:1UF604 4.4 89.2 1.0
CB C:CYS402 4.5 0.9 1.0
NAR C:1UF604 4.5 96.6 1.0
CE2 C:TYR342 4.6 0.0 1.0
CD2 C:LEU399 4.6 0.5 1.0
CZ C:TYR342 4.7 0.9 1.0
O4' C:UFP602 4.7 82.3 1.0
C1' C:UFP602 4.8 83.7 1.0
CBD C:1UF604 4.9 90.1 1.0
CD2 C:HIS403 4.9 98.6 1.0

Fluorine binding site 4 out of 5 in 4ky8

Go back to Fluorine Binding Sites List in 4ky8
Fluorine binding site 4 out of 5 in the Crystal Structure of Ts-Dhfr From Cryptosporidium Hominis in Complex with Nadph, Methotrexate, Fdump and 4-((2-Amino-6-Methyl-4-Oxo-4,7- Dihydro-3H-Pyrrolo[2,3-D]Pyrimidin-5-Yl)Thio)-2-Chlorophenyl)-L- 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, Methotrexate, Fdump and 4-((2-Amino-6-Methyl-4-Oxo-4,7- Dihydro-3H-Pyrrolo[2,3-D]Pyrimidin-5-Yl)Thio)-2-Chlorophenyl)-L- Glutamic Acid within 5.0Å range:
probe atom residue distance (Å) B Occ
D:F602

b:0.4
occ:1.00
 F5 D:UFP602 0.0 0.4 1.0
C5 D:UFP602 1.4 0.3 1.0
C6 D:UFP602 2.3 95.7 1.0
C4 D:UFP602 2.4 0.1 1.0
O4 D:UFP602 2.7 99.0 1.0
N1 D:UFP602 3.6 95.3 1.0
N3 D:UFP602 3.6 99.3 1.0
OH D:TYR342 3.9 98.5 1.0
CBB D:1UF604 4.0 0.6 1.0
CAX D:1UF604 4.0 0.5 1.0
C2 D:UFP602 4.1 97.5 1.0
CAA D:1UF604 4.1 0.8 1.0
SAS D:1UF604 4.1 0.8 1.0
SG D:CYS402 4.3 0.1 1.0
CZ2 D:TRP316 4.3 0.4 1.0
CB D:CYS402 4.3 99.2 1.0
CE2 D:TYR342 4.4 95.5 1.0
CH2 D:TRP316 4.4 0.7 1.0
CZ D:TYR342 4.5 97.5 1.0
CD2 D:HIS403 4.5 93.0 1.0
NE2 D:HIS403 4.6 96.2 1.0
CBE D:1UF604 4.7 0.4 1.0
NAR D:1UF604 4.7 0.8 1.0
O4' D:UFP602 4.7 94.3 1.0
CD2 D:LEU399 4.8 0.0 1.0
C1' D:UFP602 4.8 95.7 1.0

Fluorine binding site 5 out of 5 in 4ky8

Go back to Fluorine Binding Sites List in 4ky8
Fluorine binding site 5 out of 5 in the Crystal Structure of Ts-Dhfr From Cryptosporidium Hominis in Complex with Nadph, Methotrexate, Fdump and 4-((2-Amino-6-Methyl-4-Oxo-4,7- Dihydro-3H-Pyrrolo[2,3-D]Pyrimidin-5-Yl)Thio)-2-Chlorophenyl)-L- 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, Methotrexate, Fdump and 4-((2-Amino-6-Methyl-4-Oxo-4,7- Dihydro-3H-Pyrrolo[2,3-D]Pyrimidin-5-Yl)Thio)-2-Chlorophenyl)-L- 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 0.8 1.0
C6 E:UFP602 2.3 0.2 1.0
C4 E:UFP602 2.4 0.6 1.0
O4 E:UFP602 2.7 0.5 1.0
N1 E:UFP602 3.6 0.8 1.0
N3 E:UFP602 3.6 0.8 1.0
SAS E:1UF604 4.0 0.1 1.0
CBB E:1UF604 4.0 0.9 1.0
CAA E:1UF604 4.1 0.1 1.0
CAX E:1UF604 4.1 0.8 1.0
C2 E:UFP602 4.1 1.0 1.0
OH E:TYR342 4.1 0.3 1.0
SG E:CYS402 4.2 0.7 1.0
CB E:CYS402 4.3 0.8 1.0
CZ2 E:TRP316 4.4 0.4 1.0
CH2 E:TRP316 4.6 0.7 1.0
CD2 E:LEU399 4.7 0.9 1.0
O4' E:UFP602 4.7 0.8 1.0
CE2 E:TYR342 4.8 0.3 1.0
CBE E:1UF604 4.8 0.7 1.0
C1' E:UFP602 4.8 0.2 1.0
CZ E:TYR342 4.8 0.2 1.0
CD2 E:HIS403 4.8 0.2 1.0
NAR E:1UF604 4.8 0.1 1.0

Reference:

V.P.Kumar, K.M.Frey, Y.Wang, H.K.Jain, A.Gangjee, K.S.Anderson. Substituted Pyrrolo[2,3-D]Pyrimidines As Cryptosporidium Hominis Thymidylate Synthase Inhibitors. Bioorg.Med.Chem.Lett. V. 23 5426 2013.
ISSN: ISSN 0960-894X
PubMed: 23927969
DOI: 10.1016/J.BMCL.2013.07.037
Page generated: Sun Dec 13 12:06:37 2020

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