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Chlorine in PDB 6pf3: Crystal Structure of Human Thymidylate Synthase Delta (7-29) in Complex with Dump and 2-(4-((2-Amino-4-Oxo-4,7-Dihydro-3H-Pyrrolo[2, 3-D]Pyrimidin-5-Yl)Methyl)Benzamido)-4-Chlorobenzoic Acid

Enzymatic activity of Crystal Structure of Human Thymidylate Synthase Delta (7-29) in Complex with Dump and 2-(4-((2-Amino-4-Oxo-4,7-Dihydro-3H-Pyrrolo[2, 3-D]Pyrimidin-5-Yl)Methyl)Benzamido)-4-Chlorobenzoic Acid

All present enzymatic activity of Crystal Structure of Human Thymidylate Synthase Delta (7-29) in Complex with Dump and 2-(4-((2-Amino-4-Oxo-4,7-Dihydro-3H-Pyrrolo[2, 3-D]Pyrimidin-5-Yl)Methyl)Benzamido)-4-Chlorobenzoic Acid:
2.1.1.45;

Protein crystallography data

The structure of Crystal Structure of Human Thymidylate Synthase Delta (7-29) in Complex with Dump and 2-(4-((2-Amino-4-Oxo-4,7-Dihydro-3H-Pyrrolo[2, 3-D]Pyrimidin-5-Yl)Methyl)Benzamido)-4-Chlorobenzoic Acid, PDB code: 6pf3 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) 44.66 / 2.39
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 89.144, 89.322, 163.480, 90.00, 90.01, 90.00
R / Rfree (%) 25.7 / 28.9

Chlorine Binding Sites:

The binding sites of Chlorine atom in the Crystal Structure of Human Thymidylate Synthase Delta (7-29) in Complex with Dump and 2-(4-((2-Amino-4-Oxo-4,7-Dihydro-3H-Pyrrolo[2, 3-D]Pyrimidin-5-Yl)Methyl)Benzamido)-4-Chlorobenzoic Acid (pdb code 6pf3). 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 Human Thymidylate Synthase Delta (7-29) in Complex with Dump and 2-(4-((2-Amino-4-Oxo-4,7-Dihydro-3H-Pyrrolo[2, 3-D]Pyrimidin-5-Yl)Methyl)Benzamido)-4-Chlorobenzoic Acid, PDB code: 6pf3:
Jump to Chlorine binding site number: 1; 2; 3; 4;

Chlorine binding site 1 out of 4 in 6pf3

Go back to Chlorine Binding Sites List in 6pf3
Chlorine binding site 1 out of 4 in the Crystal Structure of Human Thymidylate Synthase Delta (7-29) in Complex with Dump and 2-(4-((2-Amino-4-Oxo-4,7-Dihydro-3H-Pyrrolo[2, 3-D]Pyrimidin-5-Yl)Methyl)Benzamido)-4-Chlorobenzoic 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 Human Thymidylate Synthase Delta (7-29) in Complex with Dump and 2-(4-((2-Amino-4-Oxo-4,7-Dihydro-3H-Pyrrolo[2, 3-D]Pyrimidin-5-Yl)Methyl)Benzamido)-4-Chlorobenzoic Acid within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl601

b:75.8
occ:1.00
 CL1 A:OE7601 0.0 75.8 1.0
C17 A:OE7601 1.7 70.7 1.0
C16 A:OE7601 2.7 70.4 1.0
C18 A:OE7601 2.7 74.6 1.0
CB A:PHE80 3.8 63.1 1.0
C19 A:OE7601 4.0 74.6 1.0
C15 A:OE7601 4.0 70.9 1.0
CG2 A:THR306 4.1 63.3 1.0
CG A:PHE80 4.3 64.3 1.0
CA A:PHE80 4.5 62.6 1.0
N A:PHE80 4.5 61.6 1.0
C20 A:OE7601 4.6 74.2 1.0
O A:ARG78 4.7 63.0 1.0
CD1 A:PHE80 4.8 66.6 1.0
CD2 A:PHE80 4.8 64.8 1.0

Chlorine binding site 2 out of 4 in 6pf3

Go back to Chlorine Binding Sites List in 6pf3
Chlorine binding site 2 out of 4 in the Crystal Structure of Human Thymidylate Synthase Delta (7-29) in Complex with Dump and 2-(4-((2-Amino-4-Oxo-4,7-Dihydro-3H-Pyrrolo[2, 3-D]Pyrimidin-5-Yl)Methyl)Benzamido)-4-Chlorobenzoic 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 Human Thymidylate Synthase Delta (7-29) in Complex with Dump and 2-(4-((2-Amino-4-Oxo-4,7-Dihydro-3H-Pyrrolo[2, 3-D]Pyrimidin-5-Yl)Methyl)Benzamido)-4-Chlorobenzoic Acid within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl601

b:76.4
occ:1.00
 CL1 B:OE7601 0.0 76.4 1.0
C17 B:OE7601 1.7 72.2 1.0
C16 B:OE7601 2.7 71.0 1.0
C18 B:OE7601 2.7 76.6 1.0
CB B:PHE80 3.9 63.9 1.0
C19 B:OE7601 4.0 75.9 1.0
C15 B:OE7601 4.0 71.2 1.0
CG2 B:THR306 4.2 65.3 1.0
CG B:PHE80 4.2 63.9 1.0
CA B:PHE80 4.5 63.5 1.0
C20 B:OE7601 4.6 73.4 1.0
N B:PHE80 4.6 63.2 1.0
CD2 B:PHE80 4.7 63.8 1.0
CD1 B:PHE80 4.8 66.1 1.0
CG2 A:THR125 4.9 85.8 1.0
O B:ARG78 4.9 64.2 1.0
O A:THR125 5.0 85.5 1.0

Chlorine binding site 3 out of 4 in 6pf3

Go back to Chlorine Binding Sites List in 6pf3
Chlorine binding site 3 out of 4 in the Crystal Structure of Human Thymidylate Synthase Delta (7-29) in Complex with Dump and 2-(4-((2-Amino-4-Oxo-4,7-Dihydro-3H-Pyrrolo[2, 3-D]Pyrimidin-5-Yl)Methyl)Benzamido)-4-Chlorobenzoic 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 Human Thymidylate Synthase Delta (7-29) in Complex with Dump and 2-(4-((2-Amino-4-Oxo-4,7-Dihydro-3H-Pyrrolo[2, 3-D]Pyrimidin-5-Yl)Methyl)Benzamido)-4-Chlorobenzoic Acid within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Cl601

b:73.8
occ:1.00
 CL1 C:OE7601 0.0 73.8 1.0
C17 C:OE7601 1.7 71.7 1.0
C16 C:OE7601 2.7 71.4 1.0
C18 C:OE7601 2.7 76.5 1.0
CB C:PHE80 3.8 63.2 1.0
C19 C:OE7601 4.0 76.3 1.0
C15 C:OE7601 4.0 72.2 1.0
CG C:PHE80 4.2 63.1 1.0
CG2 C:THR306 4.3 61.9 1.0
CA C:PHE80 4.5 62.4 1.0
C20 C:OE7601 4.6 74.0 1.0
N C:PHE80 4.6 61.8 1.0
CD2 C:PHE80 4.6 63.3 1.0
O C:HOH708 4.7 62.5 1.0
CD1 C:PHE80 4.7 65.6 1.0
O C:ARG78 5.0 63.1 1.0

Chlorine binding site 4 out of 4 in 6pf3

Go back to Chlorine Binding Sites List in 6pf3
Chlorine binding site 4 out of 4 in the Crystal Structure of Human Thymidylate Synthase Delta (7-29) in Complex with Dump and 2-(4-((2-Amino-4-Oxo-4,7-Dihydro-3H-Pyrrolo[2, 3-D]Pyrimidin-5-Yl)Methyl)Benzamido)-4-Chlorobenzoic 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 Human Thymidylate Synthase Delta (7-29) in Complex with Dump and 2-(4-((2-Amino-4-Oxo-4,7-Dihydro-3H-Pyrrolo[2, 3-D]Pyrimidin-5-Yl)Methyl)Benzamido)-4-Chlorobenzoic Acid within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Cl601

b:79.0
occ:1.00
 CL1 D:OE7601 0.0 79.0 1.0
C17 D:OE7601 1.7 71.3 1.0
C18 D:OE7601 2.7 75.7 1.0
C16 D:OE7601 2.7 70.6 1.0
CG2 D:THR306 3.8 64.8 1.0
CB D:PHE80 3.9 64.2 1.0
C19 D:OE7601 4.0 75.4 1.0
C15 D:OE7601 4.0 70.8 1.0
N D:PHE80 4.4 62.9 1.0
O D:ARG78 4.4 63.7 1.0
CA D:PHE80 4.5 63.2 1.0
CG D:PHE80 4.5 64.2 1.0
C20 D:OE7601 4.6 72.7 1.0
OG1 D:THR306 4.9 62.5 1.0
CD1 D:PHE80 5.0 66.3 1.0

Reference:

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
Page generated: Mon Jul 29 13:20:00 2024

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