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Chlorine in PDB 6cck: Crystal Structure of E.Coli Phosphopantetheine Adenylyltransferase (Ppat/Coad) in Complex with (R)-3-(3-Chlorophenyl)-3-((5-Methyl-7- Oxo-4,7-Dihydro-[1,2,4]Triazolo[1,5-A]Pyrimidin-2-Yl)Amino) Propanenitrile

Enzymatic activity of Crystal Structure of E.Coli Phosphopantetheine Adenylyltransferase (Ppat/Coad) in Complex with (R)-3-(3-Chlorophenyl)-3-((5-Methyl-7- Oxo-4,7-Dihydro-[1,2,4]Triazolo[1,5-A]Pyrimidin-2-Yl)Amino) Propanenitrile

All present enzymatic activity of Crystal Structure of E.Coli Phosphopantetheine Adenylyltransferase (Ppat/Coad) in Complex with (R)-3-(3-Chlorophenyl)-3-((5-Methyl-7- Oxo-4,7-Dihydro-[1,2,4]Triazolo[1,5-A]Pyrimidin-2-Yl)Amino) Propanenitrile:
2.7.7.3;

Protein crystallography data

The structure of Crystal Structure of E.Coli Phosphopantetheine Adenylyltransferase (Ppat/Coad) in Complex with (R)-3-(3-Chlorophenyl)-3-((5-Methyl-7- Oxo-4,7-Dihydro-[1,2,4]Triazolo[1,5-A]Pyrimidin-2-Yl)Amino) Propanenitrile, PDB code: 6cck was solved by M.Mamo, B.A.Appleton, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 42.71 / 1.61
Space group I 2 3
Cell size a, b, c (Å), α, β, γ (°) 135.050, 135.050, 135.050, 90.00, 90.00, 90.00
R / Rfree (%) 17.6 / 19.8

Other elements in 6cck:

The structure of Crystal Structure of E.Coli Phosphopantetheine Adenylyltransferase (Ppat/Coad) in Complex with (R)-3-(3-Chlorophenyl)-3-((5-Methyl-7- Oxo-4,7-Dihydro-[1,2,4]Triazolo[1,5-A]Pyrimidin-2-Yl)Amino) Propanenitrile also contains other interesting chemical elements:

Magnesium (Mg) 2 atoms

Chlorine Binding Sites:

The binding sites of Chlorine atom in the Crystal Structure of E.Coli Phosphopantetheine Adenylyltransferase (Ppat/Coad) in Complex with (R)-3-(3-Chlorophenyl)-3-((5-Methyl-7- Oxo-4,7-Dihydro-[1,2,4]Triazolo[1,5-A]Pyrimidin-2-Yl)Amino) Propanenitrile (pdb code 6cck). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 2 binding sites of Chlorine where determined in the Crystal Structure of E.Coli Phosphopantetheine Adenylyltransferase (Ppat/Coad) in Complex with (R)-3-(3-Chlorophenyl)-3-((5-Methyl-7- Oxo-4,7-Dihydro-[1,2,4]Triazolo[1,5-A]Pyrimidin-2-Yl)Amino) Propanenitrile, PDB code: 6cck:
Jump to Chlorine binding site number: 1; 2;

Chlorine binding site 1 out of 2 in 6cck

Go back to Chlorine Binding Sites List in 6cck
Chlorine binding site 1 out of 2 in the Crystal Structure of E.Coli Phosphopantetheine Adenylyltransferase (Ppat/Coad) in Complex with (R)-3-(3-Chlorophenyl)-3-((5-Methyl-7- Oxo-4,7-Dihydro-[1,2,4]Triazolo[1,5-A]Pyrimidin-2-Yl)Amino) Propanenitrile


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 E.Coli Phosphopantetheine Adenylyltransferase (Ppat/Coad) in Complex with (R)-3-(3-Chlorophenyl)-3-((5-Methyl-7- Oxo-4,7-Dihydro-[1,2,4]Triazolo[1,5-A]Pyrimidin-2-Yl)Amino) Propanenitrile within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl201

b:32.4
occ:1.00
 CL A:EXJ201 0.0 32.4 1.0
C18 A:EXJ201 1.7 24.1 1.0
C17 A:EXJ201 2.7 22.4 1.0
C19 A:EXJ201 2.7 22.9 1.0
N A:GLY9 3.5 18.2 1.0
CA A:GLY9 3.6 16.6 1.0
CE A:MET74 3.8 20.7 1.0
O A:HOH370 3.8 37.4 1.0
CB A:PRO8 3.9 17.9 1.0
C A:PRO8 3.9 20.3 1.0
C16 A:EXJ201 4.0 21.8 1.0
C20 A:EXJ201 4.0 23.2 1.0
CZ A:PHE70 4.0 18.4 1.0
C A:GLY9 4.2 19.7 1.0
O A:PRO8 4.3 19.0 1.0
CB A:ALA37 4.3 21.9 1.0
NH1 A:ARG88 4.4 29.1 1.0
O A:GLY9 4.4 19.3 1.0
SD A:MET74 4.4 22.3 1.0
CA A:PRO8 4.5 16.4 1.0
C21 A:EXJ201 4.5 21.8 1.0
CG A:PRO8 4.5 19.2 1.0
CE1 A:PHE70 4.7 18.5 1.0
O A:HOH331 4.9 49.7 1.0
N A:THR10 4.9 17.1 1.0
CE2 A:PHE70 5.0 20.3 1.0

Chlorine binding site 2 out of 2 in 6cck

Go back to Chlorine Binding Sites List in 6cck
Chlorine binding site 2 out of 2 in the Crystal Structure of E.Coli Phosphopantetheine Adenylyltransferase (Ppat/Coad) in Complex with (R)-3-(3-Chlorophenyl)-3-((5-Methyl-7- Oxo-4,7-Dihydro-[1,2,4]Triazolo[1,5-A]Pyrimidin-2-Yl)Amino) Propanenitrile


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 E.Coli Phosphopantetheine Adenylyltransferase (Ppat/Coad) in Complex with (R)-3-(3-Chlorophenyl)-3-((5-Methyl-7- Oxo-4,7-Dihydro-[1,2,4]Triazolo[1,5-A]Pyrimidin-2-Yl)Amino) Propanenitrile within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl201

b:34.1
occ:1.00
 CL B:EXJ201 0.0 34.1 1.0
C18 B:EXJ201 1.7 25.6 1.0
C17 B:EXJ201 2.7 22.0 1.0
C19 B:EXJ201 2.7 24.6 1.0
N B:GLY9 3.4 18.1 1.0
CA B:GLY9 3.4 18.1 1.0
CE B:MET74 3.7 25.2 1.0
C B:PRO8 3.8 20.2 1.0
CB B:PRO8 3.9 17.9 1.0
C B:GLY9 4.0 20.4 1.0
C16 B:EXJ201 4.0 21.3 1.0
CZ B:PHE70 4.0 18.2 1.0
C20 B:EXJ201 4.0 23.3 1.0
O B:HOH399 4.1 35.9 1.0
O B:GLY9 4.2 19.0 1.0
O B:PRO8 4.2 19.2 1.0
O B:HOH387 4.4 45.1 1.0
CA B:PRO8 4.4 16.1 1.0
C21 B:EXJ201 4.5 22.8 1.0
CG B:PRO8 4.6 19.3 1.0
CE1 B:PHE70 4.6 17.5 1.0
CB B:ALA37 4.7 21.2 1.0
N B:THR10 4.7 17.6 0.5
SD B:MET74 4.7 26.4 1.0
N B:THR10 4.7 17.3 0.5
O B:HOH339 4.7 50.0 1.0
CE2 B:PHE70 5.0 20.1 1.0

Reference:

R.J.Moreau, C.K.Skepper, B.A.Appleton, A.Blechschmidt, C.J.Balibar, B.M.Benton, J.E.Drumm, B.Y.Feng, M.Geng, C.Li, M.K.Lindvall, A.Lingel, Y.Lu, M.Mamo, W.Mergo, V.Polyakov, T.M.Smith, K.Takeoka, K.Uehara, L.Wang, J.R.Wei, A.H.Weiss, L.Xie, W.Xu, Q.Zhang, J.De Vicente. Fragment-Based Drug Discovery of Inhibitors of Phosphopantetheine Adenylyltransferase From Gram-Negative Bacteria. J. Med. Chem. V. 61 3309 2018.
ISSN: ISSN 1520-4804
PubMed: 29498517
DOI: 10.1021/ACS.JMEDCHEM.7B01691
Page generated: Fri Jul 26 23:25:39 2024

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