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Bromine in PDB 5seg: Crystal Structure of Human Phosphodiesterase 10 in Complex with 6-[(5- Bromo-1-Methyl-2-Oxopyridine-3-Carbonyl)Amino]-N-(Oxetan-3-Yl)-2- Phenyl-3H-Benzimidazole-5-Carboxamide

Enzymatic activity of Crystal Structure of Human Phosphodiesterase 10 in Complex with 6-[(5- Bromo-1-Methyl-2-Oxopyridine-3-Carbonyl)Amino]-N-(Oxetan-3-Yl)-2- Phenyl-3H-Benzimidazole-5-Carboxamide

All present enzymatic activity of Crystal Structure of Human Phosphodiesterase 10 in Complex with 6-[(5- Bromo-1-Methyl-2-Oxopyridine-3-Carbonyl)Amino]-N-(Oxetan-3-Yl)-2- Phenyl-3H-Benzimidazole-5-Carboxamide:
3.1.4.17;

Protein crystallography data

The structure of Crystal Structure of Human Phosphodiesterase 10 in Complex with 6-[(5- Bromo-1-Methyl-2-Oxopyridine-3-Carbonyl)Amino]-N-(Oxetan-3-Yl)-2- Phenyl-3H-Benzimidazole-5-Carboxamide, PDB code: 5seg was solved by C.Joseph, K.Bleicher, J.Benz, D.Schlatter, M.G.Rudolph, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 43.71 / 2.29
Space group H 3
Cell size a, b, c (Å), α, β, γ (°) 135.29, 135.29, 235.561, 90, 90, 120
R / Rfree (%) 17.4 / 23.1

Other elements in 5seg:

The structure of Crystal Structure of Human Phosphodiesterase 10 in Complex with 6-[(5- Bromo-1-Methyl-2-Oxopyridine-3-Carbonyl)Amino]-N-(Oxetan-3-Yl)-2- Phenyl-3H-Benzimidazole-5-Carboxamide also contains other interesting chemical elements:

Magnesium (Mg) 4 atoms
Zinc (Zn) 4 atoms

Bromine Binding Sites:

The binding sites of Bromine atom in the Crystal Structure of Human Phosphodiesterase 10 in Complex with 6-[(5- Bromo-1-Methyl-2-Oxopyridine-3-Carbonyl)Amino]-N-(Oxetan-3-Yl)-2- Phenyl-3H-Benzimidazole-5-Carboxamide (pdb code 5seg). 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 Human Phosphodiesterase 10 in Complex with 6-[(5- Bromo-1-Methyl-2-Oxopyridine-3-Carbonyl)Amino]-N-(Oxetan-3-Yl)-2- Phenyl-3H-Benzimidazole-5-Carboxamide, PDB code: 5seg:
Jump to Bromine binding site number: 1; 2; 3; 4;

Bromine binding site 1 out of 4 in 5seg

Go back to Bromine Binding Sites List in 5seg
Bromine binding site 1 out of 4 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with 6-[(5- Bromo-1-Methyl-2-Oxopyridine-3-Carbonyl)Amino]-N-(Oxetan-3-Yl)-2- Phenyl-3H-Benzimidazole-5-Carboxamide


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 Human Phosphodiesterase 10 in Complex with 6-[(5- Bromo-1-Methyl-2-Oxopyridine-3-Carbonyl)Amino]-N-(Oxetan-3-Yl)-2- Phenyl-3H-Benzimidazole-5-Carboxamide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Br803

b:83.4
occ:1.00
 BR33 A:IFN803 0.0 83.4 1.0
C29 A:IFN803 1.9 66.7 1.0
C28 A:IFN803 2.8 58.5 1.0
C31 A:IFN803 2.9 50.5 1.0
OG A:SER677 3.2 60.4 1.0
CD1 A:ILE692 3.7 61.6 1.0
O A:HOH927 4.0 45.0 1.0
O A:LEU675 4.0 34.8 1.0
N30 A:IFN803 4.1 60.3 1.0
C26 A:IFN803 4.1 53.5 1.0
CG1 A:VAL678 4.1 39.4 1.0
OH A:TYR524 4.1 53.1 1.0
CB A:SER677 4.2 46.6 1.0
O A:HOH936 4.3 51.9 1.0
CA A:LEU675 4.3 35.9 1.0
CD2 A:LEU675 4.5 46.4 1.0
C A:LEU675 4.5 36.5 1.0
CE2 A:PHE729 4.6 41.1 1.0
C27 A:IFN803 4.7 61.7 1.0
CZ A:PHE729 4.7 43.1 1.0
CB A:LEU675 4.8 42.0 1.0
O A:HOH960 4.9 50.9 1.0
CG1 A:ILE692 4.9 57.0 1.0
CZ A:TYR524 4.9 47.5 1.0
N A:VAL678 4.9 41.9 1.0
O A:ASP674 5.0 37.0 1.0

Bromine binding site 2 out of 4 in 5seg

Go back to Bromine Binding Sites List in 5seg
Bromine binding site 2 out of 4 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with 6-[(5- Bromo-1-Methyl-2-Oxopyridine-3-Carbonyl)Amino]-N-(Oxetan-3-Yl)-2- Phenyl-3H-Benzimidazole-5-Carboxamide


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 Human Phosphodiesterase 10 in Complex with 6-[(5- Bromo-1-Methyl-2-Oxopyridine-3-Carbonyl)Amino]-N-(Oxetan-3-Yl)-2- Phenyl-3H-Benzimidazole-5-Carboxamide within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Br803

b:88.9
occ:1.00
 BR33 B:IFN803 0.0 88.9 1.0
C29 B:IFN803 1.8 67.0 1.0
C31 B:IFN803 2.8 58.4 1.0
C28 B:IFN803 2.8 56.9 1.0
CD1 B:ILE692 3.8 51.7 1.0
O B:HOH914 3.9 43.1 1.0
OG B:SER677 4.0 69.6 1.0
CB B:SER677 4.0 51.1 1.0
O B:LEU675 4.0 38.2 1.0
C26 B:IFN803 4.0 57.5 1.0
OH B:TYR524 4.0 50.6 1.0
N30 B:IFN803 4.1 57.5 1.0
O B:HOH933 4.1 44.7 1.0
CG1 B:VAL678 4.2 40.8 1.0
CD2 B:LEU675 4.2 38.6 1.0
CA B:LEU675 4.3 35.8 1.0
C B:LEU675 4.5 39.6 1.0
C27 B:IFN803 4.6 60.7 1.0
CE2 B:PHE729 4.7 38.5 1.0
CG1 B:ILE692 4.8 52.0 1.0
O B:ASP674 4.8 40.0 1.0
CZ B:TYR524 4.8 49.5 1.0
CZ B:PHE729 4.9 44.6 1.0
CB B:LEU675 4.9 39.7 1.0
CA B:SER677 5.0 47.7 1.0
N B:SER677 5.0 43.9 1.0

Bromine binding site 3 out of 4 in 5seg

Go back to Bromine Binding Sites List in 5seg
Bromine binding site 3 out of 4 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with 6-[(5- Bromo-1-Methyl-2-Oxopyridine-3-Carbonyl)Amino]-N-(Oxetan-3-Yl)-2- Phenyl-3H-Benzimidazole-5-Carboxamide


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 Human Phosphodiesterase 10 in Complex with 6-[(5- Bromo-1-Methyl-2-Oxopyridine-3-Carbonyl)Amino]-N-(Oxetan-3-Yl)-2- Phenyl-3H-Benzimidazole-5-Carboxamide within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Br803

b:87.9
occ:1.00
 BR33 C:IFN803 0.0 87.9 1.0
C29 C:IFN803 1.9 74.7 1.0
C31 C:IFN803 2.8 61.6 1.0
C28 C:IFN803 2.8 63.5 1.0
OG C:SER677 2.9 61.7 1.0
CD1 C:ILE692 3.6 62.0 1.0
OH C:TYR524 4.0 58.8 1.0
O C:HOH961 4.0 46.5 1.0
C26 C:IFN803 4.0 63.7 1.0
N30 C:IFN803 4.1 63.1 1.0
O C:LEU675 4.2 41.2 1.0
CG1 C:VAL678 4.2 42.0 1.0
O C:HOH909 4.2 45.0 1.0
CB C:SER677 4.3 56.4 1.0
CA C:LEU675 4.3 38.7 1.0
CD2 C:LEU675 4.4 49.0 1.0
C C:LEU675 4.6 38.3 1.0
CE2 C:PHE729 4.6 57.6 1.0
C27 C:IFN803 4.7 72.8 1.0
CZ C:TYR524 4.7 48.9 1.0
O C:ASP674 4.8 43.4 1.0
CG1 C:ILE692 4.8 59.2 1.0
CZ C:PHE729 4.8 46.2 1.0
CB C:LEU675 4.8 41.7 1.0

Bromine binding site 4 out of 4 in 5seg

Go back to Bromine Binding Sites List in 5seg
Bromine binding site 4 out of 4 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with 6-[(5- Bromo-1-Methyl-2-Oxopyridine-3-Carbonyl)Amino]-N-(Oxetan-3-Yl)-2- Phenyl-3H-Benzimidazole-5-Carboxamide


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 Human Phosphodiesterase 10 in Complex with 6-[(5- Bromo-1-Methyl-2-Oxopyridine-3-Carbonyl)Amino]-N-(Oxetan-3-Yl)-2- Phenyl-3H-Benzimidazole-5-Carboxamide within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Br803

b:99.3
occ:1.00
 BR33 D:IFN803 0.0 99.3 1.0
C29 D:IFN803 1.9 79.5 1.0
C28 D:IFN803 2.8 72.8 1.0
C31 D:IFN803 2.9 66.8 1.0
OG D:SER677 3.0 64.6 1.0
O D:HOH905 3.5 44.9 1.0
CD1 D:ILE692 3.8 66.5 1.0
O D:LEU675 3.8 51.5 1.0
OH D:TYR524 4.0 67.0 1.0
CG1 D:VAL678 4.1 63.7 1.0
N30 D:IFN803 4.1 74.3 1.0
C26 D:IFN803 4.1 64.2 1.0
CA D:LEU675 4.2 53.0 1.0
C D:LEU675 4.3 53.0 1.0
CD2 D:LEU675 4.4 61.4 1.0
CB D:SER677 4.4 58.7 1.0
CE2 D:PHE729 4.6 48.9 1.0
C27 D:IFN803 4.7 65.4 1.0
CB D:LEU675 4.8 56.1 1.0
N D:VAL678 4.8 54.4 1.0
CZ D:TYR524 4.8 70.6 1.0
CG1 D:ILE692 4.8 66.4 1.0
CZ D:PHE729 4.9 55.4 1.0
N D:SER677 4.9 45.5 1.0
O D:ASP674 5.0 52.2 1.0

Reference:

A.Tosstorff, M.G.Rudolph, J.C.Cole, M.Reutlinger, C.Kramer, H.Schaffhauser, A.Nilly, A.Flohr, B.Kuhn. A High Quality, Industrial Data Set For Binding Affinity Prediction: Performance Comparison in Different Early Drug Discovery Scenarios. J.Comput.Aided Mol.Des. V. 36 753 2022.
ISSN: ESSN 1573-4951
PubMed: 36153472
DOI: 10.1007/S10822-022-00478-X
Page generated: Thu Jul 11 00:54:55 2024

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