Atomistry » Bromine » PDB 5s9u-5t6s » 5seg
Atomistry »
  Bromine »
    PDB 5s9u-5t6s »
      5seg »

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: Tue Apr 4 17:26:40 2023

Last articles

Zn in 8WB0
Zn in 8WAX
Zn in 8WAU
Zn in 8WAZ
Zn in 8WAY
Zn in 8WAV
Zn in 8WAW
Zn in 8WAT
Zn in 8W7M
Zn in 8WD3
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy