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Chlorine 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:

Fluorine (F) 5 atoms

Chlorine Binding Sites:

The binding sites of Chlorine 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 Chlorine atom.
In total 5 binding sites of Chlorine 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 Chlorine binding site number: 1; 2; 3; 4; 5;

Chlorine binding site 1 out of 5 in 4ky8

Go back to Chlorine Binding Sites List in 4ky8
Chlorine 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 Chlorine with other atoms in the Cl 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:Cl604

b:0.4
occ:1.00
 CL1 A:1UF604 0.0 0.4 1.0
CAZ A:1UF604 1.7 89.8 1.0
CAL A:1UF604 2.7 84.2 1.0
CBA A:1UF604 2.7 89.7 1.0
OAE A:1UF604 3.0 0.5 1.0
CAV A:1UF604 3.0 98.7 1.0
CD2 A:LEU429 3.5 50.7 1.0
CB A:MET519 3.8 0.4 1.0
SD A:MET519 3.8 0.6 1.0
CAY A:1UF604 4.0 84.3 1.0
CAK A:1UF604 4.0 85.4 1.0
CA A:ILE315 4.1 70.5 1.0
N A:1UF604 4.1 0.9 1.0
CG A:MET519 4.3 0.1 1.0
O A:ILE315 4.3 63.6 1.0
CE A:MET519 4.3 0.4 1.0
CB A:ILE315 4.4 59.1 1.0
CG2 A:ILE315 4.5 63.1 1.0
CAJ A:1UF604 4.5 83.5 1.0
CG A:LEU429 4.6 46.5 1.0
O A:TYR314 4.6 70.9 1.0
C A:ILE315 4.7 60.9 1.0
CA A:MET519 5.0 0.0 1.0

Chlorine binding site 2 out of 5 in 4ky8

Go back to Chlorine Binding Sites List in 4ky8
Chlorine 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 Chlorine with other atoms in the Cl 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:Cl604

b:0.8
occ:1.00
 CL1 B:1UF604 0.0 0.8 1.0
CAZ B:1UF604 1.7 99.2 1.0
CAL B:1UF604 2.7 93.6 1.0
CBA B:1UF604 2.7 99.1 1.0
CAV B:1UF604 3.0 0.0 1.0
OAE B:1UF604 3.1 0.9 1.0
SD B:MET519 3.5 1.0 1.0
CD2 B:LEU429 3.5 76.3 1.0
CB B:MET519 3.6 95.9 1.0
N B:1UF604 3.9 0.3 1.0
CAY B:1UF604 4.0 93.7 1.0
CAK B:1UF604 4.0 94.8 1.0
CG B:MET519 4.0 98.5 1.0
CE B:MET519 4.1 0.8 1.0
CA B:ILE315 4.3 90.1 1.0
O B:ILE315 4.4 0.1 1.0
CAJ B:1UF604 4.5 92.8 1.0
CB B:ILE315 4.7 93.0 1.0
CG B:LEU429 4.8 72.2 1.0
CG2 B:ILE315 4.8 97.0 1.0
O B:TYR314 4.8 0.0 1.0
C B:ILE315 4.8 94.8 1.0
CA B:MET519 4.9 97.4 1.0
CA B:1UF604 4.9 0.5 1.0

Chlorine binding site 3 out of 5 in 4ky8

Go back to Chlorine Binding Sites List in 4ky8
Chlorine 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 Chlorine with other atoms in the Cl 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:Cl604

b:0.8
occ:1.00
 CL1 C:1UF604 0.0 0.8 1.0
CAZ C:1UF604 1.7 97.3 1.0
CAL C:1UF604 2.7 91.7 1.0
CBA C:1UF604 2.7 97.2 1.0
CAV C:1UF604 3.0 0.1 1.0
OAE C:1UF604 3.1 0.9 1.0
CB C:MET519 3.6 0.5 1.0
SD C:MET519 3.7 0.7 1.0
CD1 C:LEU429 3.9 66.3 1.0
CAY C:1UF604 4.0 91.7 1.0
CAK C:1UF604 4.0 92.8 1.0
N C:1UF604 4.1 0.3 1.0
CG C:MET519 4.1 0.2 1.0
CE C:MET519 4.5 0.5 1.0
CAJ C:1UF604 4.5 90.9 1.0
CA C:ILE315 4.5 87.0 1.0
O C:ILE315 4.6 75.5 1.0
CA C:MET519 4.7 0.1 1.0
CG C:LEU429 4.8 66.6 1.0
CD2 C:LEU429 4.8 64.6 1.0
CB C:LEU429 4.8 64.6 1.0
CB C:ILE315 4.8 90.0 1.0
CG2 C:ILE315 4.9 94.0 1.0
N C:MET519 4.9 0.7 1.0
CA C:1UF604 5.0 0.5 1.0

Chlorine binding site 4 out of 5 in 4ky8

Go back to Chlorine Binding Sites List in 4ky8
Chlorine 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 Chlorine with other atoms in the Cl 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:Cl604

b:0.0
occ:1.00
 CL1 D:1UF604 0.0 0.0 1.0
CAZ D:1UF604 1.7 0.5 1.0
CAL D:1UF604 2.7 0.8 1.0
CBA D:1UF604 2.7 0.3 1.0
CAV D:1UF604 3.0 0.3 1.0
OAE D:1UF604 3.0 0.1 1.0
CD2 D:LEU429 3.4 90.6 1.0
SD D:MET519 3.5 0.1 1.0
CB D:MET519 3.6 0.9 1.0
CG D:MET519 3.9 0.6 1.0
CAY D:1UF604 4.0 0.9 1.0
CAK D:1UF604 4.0 0.0 1.0
N D:1UF604 4.0 0.5 1.0
CE D:MET519 4.2 0.9 1.0
CA D:ILE315 4.3 73.8 1.0
CAJ D:1UF604 4.5 0.1 1.0
O D:ILE315 4.5 87.9 1.0
CG D:LEU429 4.6 86.5 1.0
CB D:ILE315 4.7 76.8 1.0
CG2 D:ILE315 4.7 80.8 1.0
CA D:MET519 4.8 0.5 1.0
O D:TYR314 4.8 0.5 1.0
C D:ILE315 4.9 78.5 1.0
CA D:1UF604 5.0 0.7 1.0

Chlorine binding site 5 out of 5 in 4ky8

Go back to Chlorine Binding Sites List in 4ky8
Chlorine 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 Chlorine with other atoms in the Cl 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:Cl604

b:0.3
occ:1.00
 CL1 E:1UF604 0.0 0.3 1.0
CAZ E:1UF604 1.7 0.7 1.0
CBA E:1UF604 2.7 0.6 1.0
CAL E:1UF604 2.7 0.1 1.0
CAV E:1UF604 3.0 0.6 1.0
OAE E:1UF604 3.1 0.4 1.0
CD1 E:LEU429 3.4 0.7 1.0
CB E:MET519 3.5 0.3 1.0
SD E:MET519 3.9 0.4 1.0
CAY E:1UF604 4.0 0.2 1.0
CAK E:1UF604 4.0 0.3 1.0
N E:1UF604 4.0 0.8 1.0
CG E:MET519 4.0 1.0 1.0
CG E:LEU429 4.3 0.1 1.0
CD2 E:LEU429 4.3 0.2 1.0
CA E:MET519 4.4 0.9 1.0
CB E:LEU429 4.5 0.1 1.0
CAJ E:1UF604 4.5 0.3 1.0
N E:MET519 4.6 0.4 1.0
CE E:MET519 4.8 0.2 1.0
O E:MET517 4.9 0.4 1.0
CA E:1UF604 4.9 0.0 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 Jul 21 18:37:54 2024

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