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Chlorine in PDB 4caf: Plasmodium Vivax N-Myristoyltransferase in Complex with A Benzothiophene Inhibitor (Compound 34A)

Enzymatic activity of Plasmodium Vivax N-Myristoyltransferase in Complex with A Benzothiophene Inhibitor (Compound 34A)

All present enzymatic activity of Plasmodium Vivax N-Myristoyltransferase in Complex with A Benzothiophene Inhibitor (Compound 34A):
2.3.1.97;

Protein crystallography data

The structure of Plasmodium Vivax N-Myristoyltransferase in Complex with A Benzothiophene Inhibitor (Compound 34A), PDB code: 4caf was solved by M.D.Rackham, J.A.Brannigan, K.Rangachari, 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) 100.19 / 1.70
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 57.460, 121.100, 178.380, 90.00, 90.00, 90.00
R / Rfree (%) 15.961 / 20.495

Other elements in 4caf:

The structure of Plasmodium Vivax N-Myristoyltransferase in Complex with A Benzothiophene Inhibitor (Compound 34A) 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 Benzothiophene Inhibitor (Compound 34A) (pdb code 4caf). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 3 binding sites of Chlorine where determined in the Plasmodium Vivax N-Myristoyltransferase in Complex with A Benzothiophene Inhibitor (Compound 34A), PDB code: 4caf:
Jump to Chlorine binding site number: 1; 2; 3;

Chlorine binding site 1 out of 3 in 4caf

Go back to Chlorine Binding Sites List in 4caf
Chlorine binding site 1 out of 3 in the Plasmodium Vivax N-Myristoyltransferase in Complex with A Benzothiophene Inhibitor (Compound 34A)


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 Benzothiophene Inhibitor (Compound 34A) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl1417

b:13.5
occ:1.00
 O A:HOH2097 3.1 14.0 1.0
NZ A:LYS180 3.2 9.7 1.0
CE2 A:TYR65 3.7 10.3 1.0
CD A:LYS180 3.9 11.0 1.0
CE A:LYS180 4.1 10.7 1.0
OH A:TYR65 4.5 11.8 1.0
CD2 A:TYR65 4.6 11.2 1.0
CZ A:TYR65 4.6 10.9 1.0

Chlorine binding site 2 out of 3 in 4caf

Go back to Chlorine Binding Sites List in 4caf
Chlorine binding site 2 out of 3 in the Plasmodium Vivax N-Myristoyltransferase in Complex with A Benzothiophene Inhibitor (Compound 34A)


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 Benzothiophene Inhibitor (Compound 34A) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl1416

b:13.4
occ:1.00
 O B:HOH2340 3.0 14.4 1.0
NH2 B:ARG358 3.2 13.8 1.0
N B:LEU248 3.3 10.1 1.0
O B:HOH2336 3.3 16.2 1.0
CA B:THR247 3.7 10.5 1.0
O B:HOH2441 3.7 13.8 1.0
C B:THR247 4.0 10.7 1.0
CB B:LEU248 4.0 10.8 1.0
CG2 B:THR247 4.1 11.7 1.0
CG B:LEU248 4.1 11.1 1.0
O B:ASP246 4.1 14.6 1.0
CD1 B:LEU248 4.1 11.2 1.0
CZ B:ARG358 4.2 15.0 1.0
CA B:LEU248 4.2 11.7 1.0
NH1 B:ARG358 4.3 12.0 1.0
CB B:THR247 4.3 11.0 1.0
OG1 B:THR247 4.6 11.1 1.0
N B:THR247 4.7 12.0 1.0
C B:ASP246 4.8 12.2 1.0
O B:LEU248 4.9 12.5 1.0

Chlorine binding site 3 out of 3 in 4caf

Go back to Chlorine Binding Sites List in 4caf
Chlorine binding site 3 out of 3 in the Plasmodium Vivax N-Myristoyltransferase in Complex with A Benzothiophene Inhibitor (Compound 34A)


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 Benzothiophene Inhibitor (Compound 34A) within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Cl1415

b:14.1
occ:1.00
 NH2 C:ARG358 3.2 11.0 1.0
O C:HOH2284 3.2 17.2 1.0
N C:LEU248 3.3 13.7 1.0
CA C:THR247 3.6 12.8 1.0
O C:HOH2392 3.8 14.7 1.0
C C:THR247 3.9 13.2 1.0
CG2 C:THR247 4.0 12.1 1.0
O C:ASP246 4.1 13.8 1.0
CG C:LEU248 4.1 13.4 1.0
CB C:LEU248 4.1 13.7 1.0
CD1 C:LEU248 4.2 13.0 1.0
CZ C:ARG358 4.2 12.2 1.0
CB C:THR247 4.3 12.0 1.0
CA C:LEU248 4.3 13.2 1.0
NH1 C:ARG358 4.3 12.3 1.0
OG1 C:THR247 4.6 15.0 1.0
N C:THR247 4.6 11.7 1.0
C C:ASP246 4.8 12.4 1.0
O C:LEU248 4.9 14.3 1.0

Reference:

M.D.Rackham, J.A.Brannigan, K.Rangachari, S.Meister, A.J.Wilkinson, A.A.Holder, R.J.Leatherbarrow, E.W.Tate. Design and Synthesis of High Affinity Inhibitors of Plasmodium Falciparum and Plasmodium Vivax N- Myristoyltransferases Directed By Ligand Efficiency Dependent Lipophilicity (Lelp). J.Med.Chem. V. 57 2773 2014.
ISSN: ISSN 0022-2623
PubMed: 24641010
DOI: 10.1021/JM500066B
Page generated: Sun Jul 21 10:58:34 2024

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