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Sodium in PDB 2wp5: Trypanosoma Brucei Trypanothione Reductase in Complex with 3,4-Dihydroquinazoline Inhibitor (DDD00065414)

Enzymatic activity of Trypanosoma Brucei Trypanothione Reductase in Complex with 3,4-Dihydroquinazoline Inhibitor (DDD00065414)

All present enzymatic activity of Trypanosoma Brucei Trypanothione Reductase in Complex with 3,4-Dihydroquinazoline Inhibitor (DDD00065414):
1.8.1.12;

Protein crystallography data

The structure of Trypanosoma Brucei Trypanothione Reductase in Complex with 3,4-Dihydroquinazoline Inhibitor (DDD00065414), PDB code: 2wp5 was solved by M.S.Alphey, S.Patterson, A.H.Fairlamb, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 46.711 / 2.80
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 100.940, 63.300, 169.410, 90.00, 98.09, 90.00
R / Rfree (%) 16.42 / 21.93

Other elements in 2wp5:

The structure of Trypanosoma Brucei Trypanothione Reductase in Complex with 3,4-Dihydroquinazoline Inhibitor (DDD00065414) also contains other interesting chemical elements:

Bromine (Br) 4 atoms
Chlorine (Cl) 8 atoms

Sodium Binding Sites:

The binding sites of Sodium atom in the Trypanosoma Brucei Trypanothione Reductase in Complex with 3,4-Dihydroquinazoline Inhibitor (DDD00065414) (pdb code 2wp5). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 6 binding sites of Sodium where determined in the Trypanosoma Brucei Trypanothione Reductase in Complex with 3,4-Dihydroquinazoline Inhibitor (DDD00065414), PDB code: 2wp5:
Jump to Sodium binding site number: 1; 2; 3; 4; 5; 6;

Sodium binding site 1 out of 6 in 2wp5

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Sodium binding site 1 out of 6 in the Trypanosoma Brucei Trypanothione Reductase in Complex with 3,4-Dihydroquinazoline Inhibitor (DDD00065414)


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Trypanosoma Brucei Trypanothione Reductase in Complex with 3,4-Dihydroquinazoline Inhibitor (DDD00065414) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na1490

b:16.1
occ:1.00
 O A:THR457 2.6 10.9 1.0
O A:CYS469 2.7 12.5 1.0
O A:TYR455 3.2 13.8 1.0
C A:THR457 3.7 11.1 1.0
C A:CYS469 3.9 12.7 1.0
CA A:ILE458 3.9 9.8 1.0
N A:GLY459 3.9 10.3 1.0
CB A:CYS469 4.1 11.9 1.0
N A:ILE458 4.3 10.5 1.0
C A:TYR455 4.3 13.1 1.0
C A:ILE458 4.3 10.3 1.0
OG A:SER470 4.6 17.7 1.0
CA A:CYS469 4.7 12.6 1.0
CD1 A:TYR455 4.8 8.7 0.3
N A:SER470 4.9 13.3 1.0
CA A:GLY459 4.9 9.1 1.0
N A:THR457 4.9 12.1 1.0
CA A:THR457 4.9 11.8 1.0
CA A:TYR455 4.9 13.2 0.3
CA A:TYR455 4.9 13.3 0.3
C A:ASN456 5.0 13.0 1.0
CE1 A:TYR455 5.0 6.6 0.3
CA A:SER470 5.0 15.2 1.0
CA A:TYR455 5.0 12.6 0.3

Sodium binding site 2 out of 6 in 2wp5

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Sodium binding site 2 out of 6 in the Trypanosoma Brucei Trypanothione Reductase in Complex with 3,4-Dihydroquinazoline Inhibitor (DDD00065414)


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Trypanosoma Brucei Trypanothione Reductase in Complex with 3,4-Dihydroquinazoline Inhibitor (DDD00065414) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na1489

b:11.9
occ:1.00
 O B:THR457 2.4 9.4 1.0
O B:TYR455 2.6 12.3 1.0
O B:CYS469 3.1 16.5 1.0
C B:TYR455 3.4 12.0 1.0
C B:THR457 3.5 9.6 1.0
C B:ASN456 4.0 10.8 1.0
C B:CYS469 4.0 16.3 1.0
N B:THR457 4.1 10.6 1.0
CB B:CYS469 4.1 15.2 1.0
CA B:TYR455 4.1 12.6 1.0
N B:ASN456 4.2 11.4 1.0
N B:ILE458 4.3 9.0 1.0
CA B:ILE458 4.3 7.0 1.0
O B:ASN456 4.3 9.7 1.0
CA B:ASN456 4.4 11.0 1.0
CA B:THR457 4.4 9.7 1.0
O B:PHE454 4.5 9.8 1.0
CA B:CYS469 4.6 15.8 1.0
N B:GLY459 4.6 7.3 1.0
NH2 B:ARG472 4.8 33.1 1.0
CB B:TYR455 4.8 13.1 1.0
C B:ILE458 4.9 7.2 1.0

Sodium binding site 3 out of 6 in 2wp5

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Sodium binding site 3 out of 6 in the Trypanosoma Brucei Trypanothione Reductase in Complex with 3,4-Dihydroquinazoline Inhibitor (DDD00065414)


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Trypanosoma Brucei Trypanothione Reductase in Complex with 3,4-Dihydroquinazoline Inhibitor (DDD00065414) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na1490

b:21.0
occ:1.00
 O B:PHE114 2.5 30.1 1.0
O B:LEU120 2.6 30.0 1.0
O B:THR117 3.0 34.0 1.0
OD1 B:ASP121 3.4 35.7 1.0
C B:PHE114 3.4 30.4 1.0
C B:LEU120 3.6 30.6 1.0
O B:ASN115 4.1 31.8 1.0
C B:THR117 4.2 34.2 1.0
N B:ASN115 4.2 30.4 1.0
CA B:ASN115 4.3 30.9 1.0
C B:ASN115 4.3 31.5 1.0
CA B:PHE114 4.3 30.1 1.0
CA B:ASP121 4.4 31.5 1.0
N B:ASP121 4.4 31.0 1.0
N B:LEU120 4.4 32.2 1.0
CG B:ASP121 4.5 33.1 1.0
CA B:LEU120 4.5 31.1 1.0
N B:THR117 4.7 32.4 1.0
CB B:PHE114 4.7 29.9 1.0
CB B:LEU120 4.8 30.7 1.0
CA B:THR117 4.9 33.2 1.0

Sodium binding site 4 out of 6 in 2wp5

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Sodium binding site 4 out of 6 in the Trypanosoma Brucei Trypanothione Reductase in Complex with 3,4-Dihydroquinazoline Inhibitor (DDD00065414)


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of Trypanosoma Brucei Trypanothione Reductase in Complex with 3,4-Dihydroquinazoline Inhibitor (DDD00065414) within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Na1489

b:25.9
occ:1.00
 O C:TYR455 2.6 16.4 1.0
O C:THR457 2.8 13.2 1.0
O C:CYS469 2.9 15.7 1.0
C C:THR457 3.7 13.2 1.0
C C:TYR455 3.8 15.7 1.0
CA C:ILE458 4.1 10.2 1.0
C C:CYS469 4.1 15.5 1.0
N C:ILE458 4.3 12.0 1.0
N C:GLY459 4.4 8.8 1.0
CA C:TYR455 4.5 16.1 0.5
CA C:TYR455 4.5 16.1 0.5
C C:ASN456 4.6 15.2 1.0
CB C:CYS469 4.6 15.8 1.0
N C:THR457 4.6 14.3 1.0
C C:ILE458 4.7 9.8 1.0
N C:ASN456 4.8 15.3 1.0
CA C:THR457 4.8 13.7 1.0
O C:ASN456 4.9 15.3 1.0
CA C:CYS469 4.9 15.3 1.0
CA C:ASN456 4.9 15.6 1.0
O C:PHE454 4.9 16.1 1.0

Sodium binding site 5 out of 6 in 2wp5

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Sodium binding site 5 out of 6 in the Trypanosoma Brucei Trypanothione Reductase in Complex with 3,4-Dihydroquinazoline Inhibitor (DDD00065414)


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 5 of Trypanosoma Brucei Trypanothione Reductase in Complex with 3,4-Dihydroquinazoline Inhibitor (DDD00065414) within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Na1489

b:30.6
occ:1.00
 O D:THR457 2.6 15.2 1.0
O D:TYR455 2.6 15.4 1.0
O D:CYS469 2.7 21.2 1.0
C D:THR457 3.7 14.8 1.0
C D:TYR455 3.8 15.1 1.0
C D:CYS469 3.8 19.9 1.0
CB D:CYS469 3.9 19.1 1.0
CA D:ILE458 4.0 15.0 1.0
N D:GLY459 4.0 14.0 1.0
N D:ILE458 4.3 15.0 1.0
CA D:CYS469 4.5 19.5 1.0
C D:ILE458 4.5 14.5 1.0
CA D:TYR455 4.5 15.4 0.6
CA D:TYR455 4.5 14.8 0.4
N D:THR457 4.6 15.6 1.0
CD1 D:TYR455 4.6 12.3 0.4
C D:ASN456 4.6 15.4 1.0
CA D:THR457 4.8 15.3 1.0
N D:ASN456 4.8 15.2 1.0
O D:PHE454 4.8 15.2 1.0
N D:SER470 4.8 19.8 1.0
CE1 D:TYR455 4.8 11.0 0.4
O D:ASN456 4.9 15.4 1.0
CA D:ASN456 5.0 15.6 1.0
CG D:TYR455 5.0 12.7 0.4
CG1 D:ILE458 5.0 15.2 1.0

Sodium binding site 6 out of 6 in 2wp5

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Sodium binding site 6 out of 6 in the Trypanosoma Brucei Trypanothione Reductase in Complex with 3,4-Dihydroquinazoline Inhibitor (DDD00065414)


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 6 of Trypanosoma Brucei Trypanothione Reductase in Complex with 3,4-Dihydroquinazoline Inhibitor (DDD00065414) within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Na1490

b:46.4
occ:1.00
 O D:LEU120 2.4 15.3 1.0
O D:THR117 2.5 16.4 1.0
O D:PHE114 2.8 12.0 1.0
OD1 D:ASP121 3.0 16.8 1.0
C D:LEU120 3.4 14.9 1.0
C D:THR117 3.6 15.9 1.0
N D:LEU120 3.9 16.7 1.0
C D:PHE114 4.0 11.8 1.0
O D:ASN115 4.2 13.3 1.0
CG D:ASP121 4.2 14.6 1.0
CA D:LEU120 4.2 15.2 1.0
CA D:GLU118 4.3 17.0 1.0
N D:ASP121 4.3 13.8 1.0
N D:GLU118 4.3 16.1 1.0
N D:THR117 4.4 14.5 1.0
N D:GLY119 4.4 16.8 1.0
CA D:ASP121 4.5 12.4 1.0
CA D:THR117 4.5 15.1 1.0
C D:ASN115 4.5 13.3 1.0
C D:GLU118 4.6 16.7 1.0
CA D:ASN115 4.7 13.1 1.0
CB D:LEU120 4.7 15.0 1.0
N D:ASN115 4.8 12.4 1.0
CB D:ASP121 4.8 12.8 1.0
CA D:PHE114 4.9 11.0 1.0
C D:GLY119 5.0 17.5 1.0

Reference:

S.Patterson, M.S.Alphey, D.C.Jones, E.J.Shanks, I.P.Street, J.A.Frearson, P.G.Wyatt, I.H.Gilbert, A.H.Fairlamb. Dihydroquinazolines As A Novel Class of Trypanosoma Brucei Trypanothione Reductase Inhibitors: Discovery, Synthesis, and Characterization of Their Binding Mode By Protein Crystallography. J.Med.Chem. V. 54 6514 2011.
ISSN: ISSN 0022-2623
PubMed: 21851087
DOI: 10.1021/JM200312V
Page generated: Mon Oct 7 04:51:36 2024

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