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Chlorine in PDB 5t0l: Crystal Structure of Toxoplasma Gondii Ts-Dhfr Complexed with Nadph, Dump, Pddf and 5-(4-(3,4-Dichlorophenyl)Piperazin-1-Yl)Pyrimidine-2, 4-Diamine (Trc-15)

Enzymatic activity of Crystal Structure of Toxoplasma Gondii Ts-Dhfr Complexed with Nadph, Dump, Pddf and 5-(4-(3,4-Dichlorophenyl)Piperazin-1-Yl)Pyrimidine-2, 4-Diamine (Trc-15)

All present enzymatic activity of Crystal Structure of Toxoplasma Gondii Ts-Dhfr Complexed with Nadph, Dump, Pddf and 5-(4-(3,4-Dichlorophenyl)Piperazin-1-Yl)Pyrimidine-2, 4-Diamine (Trc-15):
1.5.1.3; 2.1.1.45;

Protein crystallography data

The structure of Crystal Structure of Toxoplasma Gondii Ts-Dhfr Complexed with Nadph, Dump, Pddf and 5-(4-(3,4-Dichlorophenyl)Piperazin-1-Yl)Pyrimidine-2, 4-Diamine (Trc-15), PDB code: 5t0l was solved by S.B.Thomas, Z.Chen, H.Lu, Y.Li, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 109.93 / 3.13
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 51.277, 143.983, 170.214, 90.00, 90.00, 90.00
R / Rfree (%) 25.3 / 27.4

Chlorine Binding Sites:

The binding sites of Chlorine atom in the Crystal Structure of Toxoplasma Gondii Ts-Dhfr Complexed with Nadph, Dump, Pddf and 5-(4-(3,4-Dichlorophenyl)Piperazin-1-Yl)Pyrimidine-2, 4-Diamine (Trc-15) (pdb code 5t0l). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 4 binding sites of Chlorine where determined in the Crystal Structure of Toxoplasma Gondii Ts-Dhfr Complexed with Nadph, Dump, Pddf and 5-(4-(3,4-Dichlorophenyl)Piperazin-1-Yl)Pyrimidine-2, 4-Diamine (Trc-15), PDB code: 5t0l:
Jump to Chlorine binding site number: 1; 2; 3; 4;

Chlorine binding site 1 out of 4 in 5t0l

Go back to Chlorine Binding Sites List in 5t0l
Chlorine binding site 1 out of 4 in the Crystal Structure of Toxoplasma Gondii Ts-Dhfr Complexed with Nadph, Dump, Pddf and 5-(4-(3,4-Dichlorophenyl)Piperazin-1-Yl)Pyrimidine-2, 4-Diamine (Trc-15)


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 Toxoplasma Gondii Ts-Dhfr Complexed with Nadph, Dump, Pddf and 5-(4-(3,4-Dichlorophenyl)Piperazin-1-Yl)Pyrimidine-2, 4-Diamine (Trc-15) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl704

b:32.9
occ:0.60
 CL1 A:73X704 0.0 32.9 0.6
C2 A:73X704 1.8 31.0 0.6
C3 A:73X704 2.7 31.1 0.6
C1 A:73X704 2.8 30.2 0.6
CL A:73X704 3.1 35.0 0.6
CD A:PRO88 3.5 79.1 1.0
CG A:PRO88 3.6 79.9 1.0
CD2 A:PHE91 3.8 99.5 1.0
CG A:PHE91 3.8 99.9 1.0
CB A:PHE91 3.9 96.3 1.0
C4 A:73X704 4.0 29.7 0.6
CE1 A:PHE32 4.0 81.3 1.0
C A:73X704 4.1 29.2 0.6
CE2 A:PHE91 4.4 99.9 1.0
CD1 A:PHE91 4.5 0.7 1.0
C5 A:73X704 4.6 28.6 0.6
CZ A:PHE32 4.7 82.5 1.0
N A:PRO88 4.8 81.0 1.0
CD1 A:PHE32 4.9 80.1 1.0

Chlorine binding site 2 out of 4 in 5t0l

Go back to Chlorine Binding Sites List in 5t0l
Chlorine binding site 2 out of 4 in the Crystal Structure of Toxoplasma Gondii Ts-Dhfr Complexed with Nadph, Dump, Pddf and 5-(4-(3,4-Dichlorophenyl)Piperazin-1-Yl)Pyrimidine-2, 4-Diamine (Trc-15)


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 Toxoplasma Gondii Ts-Dhfr Complexed with Nadph, Dump, Pddf and 5-(4-(3,4-Dichlorophenyl)Piperazin-1-Yl)Pyrimidine-2, 4-Diamine (Trc-15) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl704

b:35.0
occ:0.60
 CL A:73X704 0.0 35.0 0.6
C3 A:73X704 1.8 31.1 0.6
C2 A:73X704 2.7 31.0 0.6
C4 A:73X704 2.8 29.7 0.6
CD A:PRO88 2.8 79.1 1.0
CL1 A:73X704 3.1 32.9 0.6
CA A:MET87 3.6 76.4 1.0
CG A:PRO88 3.9 79.9 1.0
O A:SER86 3.9 74.5 1.0
N A:PRO88 3.9 81.0 1.0
C1 A:73X704 4.0 30.2 0.6
C5 A:73X704 4.1 28.6 0.6
C A:MET87 4.3 78.4 1.0
N A:MET87 4.3 75.3 1.0
CB A:MET87 4.4 75.4 1.0
C A:SER86 4.4 75.2 1.0
CG A:MET87 4.4 77.2 1.0
C A:73X704 4.5 29.2 0.6

Chlorine binding site 3 out of 4 in 5t0l

Go back to Chlorine Binding Sites List in 5t0l
Chlorine binding site 3 out of 4 in the Crystal Structure of Toxoplasma Gondii Ts-Dhfr Complexed with Nadph, Dump, Pddf and 5-(4-(3,4-Dichlorophenyl)Piperazin-1-Yl)Pyrimidine-2, 4-Diamine (Trc-15)


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 Toxoplasma Gondii Ts-Dhfr Complexed with Nadph, Dump, Pddf and 5-(4-(3,4-Dichlorophenyl)Piperazin-1-Yl)Pyrimidine-2, 4-Diamine (Trc-15) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl704

b:35.1
occ:0.60
 CL1 B:73X704 0.0 35.1 0.6
C2 B:73X704 1.8 32.0 0.6
C1 B:73X704 2.7 31.0 0.6
C3 B:73X704 2.8 31.9 0.6
CD B:PRO88 2.9 94.8 1.0
CG B:PRO88 3.2 94.3 1.0
CL B:73X704 3.2 35.6 0.6
C4 B:73X704 4.0 30.5 0.6
C B:73X704 4.0 29.9 0.6
N B:PRO88 4.3 95.3 1.0
CD2 B:PHE91 4.5 0.1 1.0
CE1 B:PHE32 4.5 0.3 1.0
C5 B:73X704 4.6 29.4 0.6
CB B:PRO88 4.6 95.0 1.0
CZ B:PHE32 4.6 0.5 1.0
CA B:MET87 4.7 94.8 1.0

Chlorine binding site 4 out of 4 in 5t0l

Go back to Chlorine Binding Sites List in 5t0l
Chlorine binding site 4 out of 4 in the Crystal Structure of Toxoplasma Gondii Ts-Dhfr Complexed with Nadph, Dump, Pddf and 5-(4-(3,4-Dichlorophenyl)Piperazin-1-Yl)Pyrimidine-2, 4-Diamine (Trc-15)


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 Toxoplasma Gondii Ts-Dhfr Complexed with Nadph, Dump, Pddf and 5-(4-(3,4-Dichlorophenyl)Piperazin-1-Yl)Pyrimidine-2, 4-Diamine (Trc-15) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl704

b:35.6
occ:0.60
 CL B:73X704 0.0 35.6 0.6
C3 B:73X704 1.8 31.9 0.6
C4 B:73X704 2.8 30.5 0.6
C2 B:73X704 2.8 32.0 0.6
CL1 B:73X704 3.2 35.1 0.6
O B:SER86 3.7 96.3 1.0
C5 B:73X704 4.1 29.4 0.6
C1 B:73X704 4.1 31.0 0.6
CD B:PRO88 4.1 94.8 1.0
CD1 B:LEU23 4.4 64.5 1.0
CG B:LEU23 4.4 64.0 1.0
C B:SER86 4.5 95.6 1.0
C B:73X704 4.6 29.9 0.6
CA B:MET87 4.7 94.8 1.0
N B:MET87 4.9 95.1 1.0

Reference:

M.E.Welsch, J.Zhou, Y.Gao, Y.Yan, G.Porter, G.Agnihotri, Y.Li, H.Lu, Z.Chen, S.B.Thomas. Discovery of Potent and Selective Leads Against Toxoplasma Gondii Dihydrofolate Reductase Via Structure-Based Design. Acs Med Chem Lett V. 7 1124 2016.
ISSN: ISSN 1948-5875
PubMed: 27994750
DOI: 10.1021/ACSMEDCHEMLETT.6B00328
Page generated: Fri Jul 26 17:14:34 2024

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