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Chlorine in PDB 4ufx: Plasmodium Vivax N-Myristoyltransferase in Complex with A Pyridyl Inhibitor (Compound 19)

Enzymatic activity of Plasmodium Vivax N-Myristoyltransferase in Complex with A Pyridyl Inhibitor (Compound 19)

All present enzymatic activity of Plasmodium Vivax N-Myristoyltransferase in Complex with A Pyridyl Inhibitor (Compound 19):
2.3.1.97;

Protein crystallography data

The structure of Plasmodium Vivax N-Myristoyltransferase in Complex with A Pyridyl Inhibitor (Compound 19), PDB code: 4ufx was solved by Z.Yu, J.A.Brannigan, K.Rangachari, W.P.Heal, A.J.Wilkinson, A.A.Holder, E.W.Tate, R.J.Leatherbarrow, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 98.32 / 1.49
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 57.328, 118.891, 174.895, 90.00, 90.00, 90.00
R / Rfree (%) 15.82 / 19.664

Other elements in 4ufx:

The structure of Plasmodium Vivax N-Myristoyltransferase in Complex with A Pyridyl Inhibitor (Compound 19) also contains other interesting chemical elements:

Magnesium (Mg) 3 atoms

Chlorine Binding Sites:

The binding sites of Chlorine atom in the Plasmodium Vivax N-Myristoyltransferase in Complex with A Pyridyl Inhibitor (Compound 19) (pdb code 4ufx). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 6 binding sites of Chlorine where determined in the Plasmodium Vivax N-Myristoyltransferase in Complex with A Pyridyl Inhibitor (Compound 19), PDB code: 4ufx:
Jump to Chlorine binding site number: 1; 2; 3; 4; 5; 6;

Chlorine binding site 1 out of 6 in 4ufx

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Chlorine binding site 1 out of 6 in the Plasmodium Vivax N-Myristoyltransferase in Complex with A Pyridyl Inhibitor (Compound 19)


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of Plasmodium Vivax N-Myristoyltransferase in Complex with A Pyridyl Inhibitor (Compound 19) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl1413

b:9.7
occ:1.00
 NH2 A:ARG358 3.2 10.5 1.0
O A:HOH2412 3.3 11.2 1.0
N A:LEU248 3.3 7.2 1.0
CA A:THR247 3.7 8.8 1.0
CB A:LEU248 4.0 8.5 1.0
C A:THR247 4.0 7.9 1.0
CG A:LEU248 4.1 8.4 1.0
O A:ASP246 4.1 9.9 1.0
CG2 A:THR247 4.1 9.9 1.0
CD1 A:LEU248 4.2 9.7 1.0
CZ A:ARG358 4.2 9.9 1.0
NH1 A:ARG358 4.2 9.7 1.0
CA A:LEU248 4.3 8.1 1.0
CB A:THR247 4.4 10.0 1.0
OG1 A:THR247 4.7 9.2 1.0
N A:THR247 4.7 8.5 1.0
C A:ASP246 4.8 9.2 1.0
O A:LEU248 4.9 10.2 1.0

Chlorine binding site 2 out of 6 in 4ufx

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Chlorine binding site 2 out of 6 in the Plasmodium Vivax N-Myristoyltransferase in Complex with A Pyridyl Inhibitor (Compound 19)


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of Plasmodium Vivax N-Myristoyltransferase in Complex with A Pyridyl Inhibitor (Compound 19) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl1414

b:13.6
occ:1.00
 O B:HOH2435 3.1 11.1 1.0
O A:HOH2458 3.2 21.7 1.0
O A:HOH2567 3.2 24.5 1.0
O A:HOH2574 3.2 12.7 1.0
N A:ALA401 3.3 8.2 1.0
CD2 A:HIS404 3.7 10.5 1.0
CA A:PHE400 3.8 8.9 1.0
CB A:PHE400 3.9 9.4 1.0
CB A:ALA401 3.9 8.7 1.0
NE2 A:HIS404 4.0 10.8 1.0
CA B:GLN371 4.0 11.0 1.0
C A:PHE400 4.0 8.0 1.0
CA A:ALA401 4.2 7.2 1.0
CB B:GLN371 4.3 15.2 1.0
O B:MET370 4.3 10.6 1.0
CG B:GLN371 4.4 19.0 1.0
O B:HOH2434 4.7 12.0 1.0
O A:SER399 4.8 14.4 1.0
O A:HOH2457 4.8 15.7 0.5
C B:GLN371 4.9 9.7 1.0
O A:HOH2570 4.9 19.0 1.0
N B:GLN371 5.0 9.3 1.0
O B:GLN371 5.0 10.8 1.0
C B:MET370 5.0 8.8 1.0
CG A:HIS404 5.0 9.4 1.0

Chlorine binding site 3 out of 6 in 4ufx

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Chlorine binding site 3 out of 6 in the Plasmodium Vivax N-Myristoyltransferase in Complex with A Pyridyl Inhibitor (Compound 19)


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 3 of Plasmodium Vivax N-Myristoyltransferase in Complex with A Pyridyl Inhibitor (Compound 19) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl1415

b:39.9
occ:1.00
 O A:ILE222 2.7 12.0 1.0
O A:SER227 2.7 19.7 1.0
CA A:GLY225 3.5 19.0 1.0
CG2 A:ILE222 3.5 11.0 0.5
C A:ILE222 3.6 10.5 1.0
CA A:ILE222 3.8 11.0 0.5
C A:SER227 3.8 21.2 1.0
CA A:ILE222 3.8 11.0 0.5
O A:HOH2386 4.0 31.1 1.0
N A:GLY225 4.0 13.8 1.0
CG2 A:ILE222 4.1 10.6 0.5
CA A:SER228 4.2 23.9 1.0
CB A:ILE222 4.2 10.6 0.5
C A:GLY225 4.3 20.3 1.0
CB A:SER228 4.4 31.2 1.0
N A:SER228 4.5 25.1 1.0
O A:LEU221 4.6 10.2 1.0
CB A:ILE222 4.6 10.5 0.5
N A:SER227 4.7 19.3 1.0
CD1 A:ILE222 4.8 11.3 0.5
N A:GLU223 4.8 9.2 1.0
N A:PHE226 4.8 17.6 1.0
O A:GLY225 4.9 23.1 1.0
CG1 A:ILE222 5.0 11.5 0.5
CA A:SER227 5.0 19.7 1.0

Chlorine binding site 4 out of 6 in 4ufx

Go back to Chlorine Binding Sites List in 4ufx
Chlorine binding site 4 out of 6 in the Plasmodium Vivax N-Myristoyltransferase in Complex with A Pyridyl Inhibitor (Compound 19)


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 4 of Plasmodium Vivax N-Myristoyltransferase in Complex with A Pyridyl Inhibitor (Compound 19) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl1413

b:10.4
occ:1.00
 O B:HOH2063 3.2 18.4 1.0
NZ B:LYS180 3.3 9.4 1.0
CE1 B:TYR65 3.7 9.3 1.0
CD B:LYS180 3.9 9.1 1.0
CE B:LYS180 4.1 8.8 1.0
CD1 B:TYR65 4.5 9.1 1.0
OH B:TYR65 4.6 10.5 1.0
CZ B:TYR65 4.7 9.0 1.0

Chlorine binding site 5 out of 6 in 4ufx

Go back to Chlorine Binding Sites List in 4ufx
Chlorine binding site 5 out of 6 in the Plasmodium Vivax N-Myristoyltransferase in Complex with A Pyridyl Inhibitor (Compound 19)


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 5 of Plasmodium Vivax N-Myristoyltransferase in Complex with A Pyridyl Inhibitor (Compound 19) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl1414

b:14.0
occ:1.00
 O A:HOH2542 3.1 32.0 1.0
O A:HOH2540 3.2 11.2 1.0
O B:HOH2026 3.2 25.1 1.0
O A:HOH2538 3.2 11.9 1.0
N B:ALA401 3.3 8.4 1.0
CA B:PHE400 3.8 10.4 1.0
CD2 B:HIS404 3.8 10.9 1.0
CB B:ALA401 3.8 9.2 1.0
CA A:GLN371 3.9 10.2 1.0
NE2 B:HIS404 4.0 13.7 1.0
CB B:PHE400 4.0 10.9 1.0
C B:PHE400 4.0 9.1 1.0
CA B:ALA401 4.2 7.9 1.0
CB A:GLN371 4.2 12.0 1.0
CG A:GLN371 4.2 18.4 1.0
O A:MET370 4.2 8.7 1.0
O A:HOH2539 4.7 13.0 1.0
O A:HOH2544 4.8 20.9 1.0
O B:SER399 4.9 15.4 1.0
C A:GLN371 4.9 8.4 1.0
N A:GLN371 4.9 9.3 1.0
C A:MET370 4.9 7.9 1.0
OE2 B:GLU45 4.9 43.8 0.5
O A:GLN371 5.0 8.7 1.0

Chlorine binding site 6 out of 6 in 4ufx

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Chlorine binding site 6 out of 6 in the Plasmodium Vivax N-Myristoyltransferase in Complex with A Pyridyl Inhibitor (Compound 19)


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 6 of Plasmodium Vivax N-Myristoyltransferase in Complex with A Pyridyl Inhibitor (Compound 19) within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Cl1412

b:9.4
occ:1.00
 O C:HOH2094 3.1 12.7 1.0
NZ C:LYS180 3.3 8.9 1.0
CE2 C:TYR65 3.7 8.6 1.0
O C:HOH2095 3.8 12.7 1.0
CD C:LYS180 3.9 7.5 1.0
CE C:LYS180 4.1 8.0 1.0
OH C:TYR65 4.5 9.2 1.0
CD2 C:TYR65 4.5 8.5 1.0
CZ C:TYR65 4.6 8.1 1.0

Reference:

Z.Yu, J.A.Brannigan, K.Rangachari, W.P.Heal, A.J.Wilkinson, A.A.Holder, R.J.Leatherbarrow, E.W.Tate. Discovery of Pyridyl-Based Inhibitors of Plasmodium Falciparum N-Myristoyltransferase Medchemcomm V. 6 1767 2015.
ISSN: ISSN 2040-2503
PubMed: 26962430
DOI: 10.1039/C5MD00242G
Page generated: Fri Jul 26 02:16:22 2024

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