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Bromine in PDB 6bm7: Crystal Structure of Trypanosoma Brucei Adometdc/Prozyme Heterodimer in Complex with Pyrimidineamine Inhibitor UTSAM568

Enzymatic activity of Crystal Structure of Trypanosoma Brucei Adometdc/Prozyme Heterodimer in Complex with Pyrimidineamine Inhibitor UTSAM568

All present enzymatic activity of Crystal Structure of Trypanosoma Brucei Adometdc/Prozyme Heterodimer in Complex with Pyrimidineamine Inhibitor UTSAM568:
4.1.1.50;

Protein crystallography data

The structure of Crystal Structure of Trypanosoma Brucei Adometdc/Prozyme Heterodimer in Complex with Pyrimidineamine Inhibitor UTSAM568, PDB code: 6bm7 was solved by O.A.Volkov, Z.Chen, M.A.Phillips, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 48.26 / 2.98
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 81.090, 96.250, 98.840, 90.00, 102.43, 90.00
R / Rfree (%) 20 / 25.5

Bromine Binding Sites:

The binding sites of Bromine atom in the Crystal Structure of Trypanosoma Brucei Adometdc/Prozyme Heterodimer in Complex with Pyrimidineamine Inhibitor UTSAM568 (pdb code 6bm7). This binding sites where shown within 5.0 Angstroms radius around Bromine atom.
In total 4 binding sites of Bromine where determined in the Crystal Structure of Trypanosoma Brucei Adometdc/Prozyme Heterodimer in Complex with Pyrimidineamine Inhibitor UTSAM568, PDB code: 6bm7:
Jump to Bromine binding site number: 1; 2; 3; 4;

Bromine binding site 1 out of 4 in 6bm7

Go back to Bromine Binding Sites List in 6bm7
Bromine binding site 1 out of 4 in the Crystal Structure of Trypanosoma Brucei Adometdc/Prozyme Heterodimer in Complex with Pyrimidineamine Inhibitor UTSAM568


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 1 of Crystal Structure of Trypanosoma Brucei Adometdc/Prozyme Heterodimer in Complex with Pyrimidineamine Inhibitor UTSAM568 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Br402

b:0.6
occ:1.00
 BR9 B:DY7402 0.0 0.6 1.0
C08 B:DY7402 2.0 69.8 1.0
HG B:SER249 2.5 87.1 1.0
C10 B:DY7402 2.9 68.8 1.0
C07 B:DY7402 2.9 72.4 1.0
HB3 B:HIS262 2.9 55.8 1.0
H071 B:DY7402 2.9 86.9 1.0
H B:ILE263 3.0 66.0 1.0
H101 B:DY7402 3.0 82.5 1.0
OG B:SER249 3.1 72.6 1.0
HD1 B:HIS262 3.2 62.4 1.0
O B:ILE263 3.5 57.8 1.0
O B:TYR248 3.6 58.6 1.0
N B:ILE263 3.6 55.0 1.0
HA B:HIS262 3.7 58.1 1.0
CB B:HIS262 3.8 46.5 1.0
H B:TYR248 3.8 73.1 1.0
ND1 B:HIS262 3.9 52.0 1.0
C B:TYR248 4.1 63.1 1.0
CA B:HIS262 4.1 48.4 1.0
C B:ILE263 4.1 54.2 1.0
C B:HIS262 4.2 51.1 1.0
C11 B:DY7402 4.2 77.2 1.0
C06 B:DY7402 4.3 72.0 1.0
CG B:HIS262 4.3 42.6 1.0
CB B:SER249 4.3 55.4 1.0
N B:TYR248 4.3 60.9 1.0
HA B:SER249 4.3 65.0 1.0
HE1 B:TYR243 4.5 84.4 1.0
CA B:ILE263 4.5 53.0 1.0
HB2 B:HIS262 4.5 55.8 1.0
N B:SER249 4.5 64.2 1.0
CA B:SER249 4.6 54.2 1.0
HB3 B:SER249 4.6 66.4 1.0
SG B:CYS100 4.7 59.6 1.0
CE1 B:TYR243 4.7 70.4 1.0
C13 B:DY7402 4.8 76.8 1.0
HG B:CYS100 4.8 71.5 1.0
HE2 A:PHE28 4.8 63.7 1.0
HA2 B:GLY247 4.8 74.0 1.0
HA3 B:GLY247 4.8 74.0 1.0
CA B:TYR248 4.9 62.1 1.0

Bromine binding site 2 out of 4 in 6bm7

Go back to Bromine Binding Sites List in 6bm7
Bromine binding site 2 out of 4 in the Crystal Structure of Trypanosoma Brucei Adometdc/Prozyme Heterodimer in Complex with Pyrimidineamine Inhibitor UTSAM568


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 2 of Crystal Structure of Trypanosoma Brucei Adometdc/Prozyme Heterodimer in Complex with Pyrimidineamine Inhibitor UTSAM568 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Br402

b:1.0
occ:1.00
 BR2 B:DY7402 0.0 1.0 1.0
C11 B:DY7402 2.0 77.2 1.0
C13 B:DY7402 2.9 76.8 1.0
C10 B:DY7402 2.9 68.8 1.0
H131 B:DY7402 2.9 92.2 1.0
H101 B:DY7402 3.0 82.5 1.0
HG B:CYS100 3.1 71.5 1.0
HB2 A:GLU85 3.2 81.4 1.0
H A:GLU85 3.4 81.7 1.0
HA A:SER84 3.6 79.8 1.0
N A:GLU85 3.7 68.1 1.0
SG B:CYS100 3.8 59.6 1.0
O3 B:PYR86 3.9 48.3 1.0
HH B:TYR243 4.0 74.3 1.0
CB A:GLU85 4.1 67.8 1.0
H B:CYS100 4.2 59.5 1.0
C08 B:DY7402 4.2 69.8 1.0
C A:SER84 4.2 64.1 1.0
C06 B:DY7402 4.3 72.0 1.0
HA A:GLU85 4.3 82.7 1.0
O A:LEU83 4.3 65.3 1.0
CA A:GLU85 4.3 68.9 1.0
CA A:SER84 4.3 66.5 1.0
HZ A:PHE28 4.3 66.9 1.0
OE1 A:GLU85 4.4 78.7 1.0
C2 B:PYR86 4.4 51.7 1.0
C3 B:PYR86 4.4 58.4 1.0
HB3 A:GLU85 4.5 81.4 1.0
OH B:TYR243 4.5 61.9 1.0
HE2 B:TYR243 4.7 79.6 1.0
C07 B:DY7402 4.8 72.4 1.0
O B:CYS100 4.8 51.7 1.0
HG13 B:ILE103 4.8 70.5 1.0
C A:LEU83 4.8 59.7 1.0
N A:SER84 4.9 59.1 1.0

Bromine binding site 3 out of 4 in 6bm7

Go back to Bromine Binding Sites List in 6bm7
Bromine binding site 3 out of 4 in the Crystal Structure of Trypanosoma Brucei Adometdc/Prozyme Heterodimer in Complex with Pyrimidineamine Inhibitor UTSAM568


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 3 of Crystal Structure of Trypanosoma Brucei Adometdc/Prozyme Heterodimer in Complex with Pyrimidineamine Inhibitor UTSAM568 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Br402

b:0.3
occ:1.00
 BR9 D:DY7402 0.0 0.3 1.0
C08 D:DY7402 2.0 90.6 1.0
HG D:SER249 2.6 73.7 1.0
HB3 D:HIS262 2.8 60.1 1.0
C07 D:DY7402 2.9 85.0 1.0
H071 D:DY7402 2.9 0.0 1.0
C10 D:DY7402 2.9 89.2 1.0
H101 D:DY7402 3.0 0.1 1.0
HD1 D:HIS262 3.3 60.6 1.0
OG D:SER249 3.3 61.4 1.0
H D:ILE263 3.5 62.7 1.0
CB D:HIS262 3.7 50.1 1.0
HA D:HIS262 3.7 49.5 1.0
ND1 D:HIS262 3.9 50.5 1.0
O D:ILE263 4.0 45.9 1.0
N D:ILE263 4.0 52.3 1.0
H D:TYR248 4.0 57.1 1.0
HE1 D:TYR243 4.0 80.8 1.0
CA D:HIS262 4.1 41.3 1.0
O D:TYR248 4.1 49.0 1.0
C11 D:DY7402 4.2 90.8 1.0
CG D:HIS262 4.2 47.4 1.0
C06 D:DY7402 4.3 85.7 1.0
C D:HIS262 4.3 43.7 1.0
C D:TYR248 4.4 54.0 1.0
HB2 D:HIS262 4.4 60.1 1.0
CB D:SER249 4.5 56.2 1.0
CE1 D:TYR243 4.5 67.3 1.0
HA D:SER249 4.5 58.5 1.0
N D:TYR248 4.5 47.6 1.0
C D:ILE263 4.6 43.9 1.0
N D:SER249 4.6 54.4 1.0
HE2 C:PHE28 4.6 80.8 1.0
HB3 D:SER249 4.6 67.5 1.0
SG D:CYS100 4.7 67.4 1.0
C13 D:DY7402 4.7 86.6 1.0
CA D:SER249 4.8 48.7 1.0
HA3 D:GLY247 4.9 62.0 1.0
CA D:ILE263 4.9 46.1 1.0
HG D:CYS100 5.0 80.9 1.0
HA2 D:GLY247 5.0 62.0 1.0
HD1 D:TYR243 5.0 75.7 1.0

Bromine binding site 4 out of 4 in 6bm7

Go back to Bromine Binding Sites List in 6bm7
Bromine binding site 4 out of 4 in the Crystal Structure of Trypanosoma Brucei Adometdc/Prozyme Heterodimer in Complex with Pyrimidineamine Inhibitor UTSAM568


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 4 of Crystal Structure of Trypanosoma Brucei Adometdc/Prozyme Heterodimer in Complex with Pyrimidineamine Inhibitor UTSAM568 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Br402

b:0.1
occ:1.00
 BR2 D:DY7402 0.0 0.1 1.0
C11 D:DY7402 2.0 90.8 1.0
H C:GLU85 2.8 88.9 1.0
C13 D:DY7402 2.9 86.6 1.0
C10 D:DY7402 2.9 89.2 1.0
H131 D:DY7402 2.9 0.9 1.0
H101 D:DY7402 3.0 0.1 1.0
HG D:CYS100 3.0 80.9 1.0
HB2 C:GLU85 3.2 99.7 1.0
HA C:SER84 3.3 80.9 1.0
N C:GLU85 3.5 74.1 1.0
O3 D:PYR86 3.9 60.0 1.0
SG D:CYS100 3.9 67.4 1.0
CB C:GLU85 4.0 83.0 1.0
CA C:SER84 4.1 67.4 1.0
HZ C:PHE28 4.1 84.0 1.0
H D:CYS100 4.2 60.9 1.0
C C:SER84 4.2 68.5 1.0
C08 D:DY7402 4.2 90.6 1.0
CA C:GLU85 4.2 76.5 1.0
C06 D:DY7402 4.2 85.7 1.0
HB3 C:GLU85 4.3 99.7 1.0
O C:LEU83 4.4 63.3 1.0
HA C:GLU85 4.4 91.8 1.0
HG13 D:ILE103 4.5 61.4 1.0
HD11 D:ILE103 4.6 79.0 1.0
N C:SER84 4.7 63.2 1.0
C07 D:DY7402 4.7 85.0 1.0
O D:CYS100 4.8 52.4 1.0
C C:LEU83 4.8 60.5 1.0
HH D:TYR243 4.8 87.9 1.0
OE2 C:GLU85 4.9 70.3 1.0
C2 D:PYR86 4.9 53.7 1.0
HG12 D:ILE103 5.0 61.4 1.0
N D:CYS100 5.0 50.8 1.0
CZ C:PHE28 5.0 70.0 1.0

Reference:

O.A.Volkov, A.J.Brockway, S.A.Wring, M.Peel, Z.Chen, M.A.Phillips, J.K.De Brabander. Species-Selective Pyrimidineamine Inhibitors of Trypanosoma Brucei S-Adenosylmethionine Decarboxylase. J. Med. Chem. V. 61 1182 2018.
ISSN: ISSN 1520-4804
PubMed: 29271204
DOI: 10.1021/ACS.JMEDCHEM.7B01654
Page generated: Thu Jul 11 01:29:55 2024

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