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Zinc 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:

Bromine (Br) 4 atoms
Magnesium (Mg) 4 atoms

Zinc Binding Sites:

The binding sites of Zinc 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 Zinc atom.
In total 4 binding sites of Zinc 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 Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in 5seg

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Zinc 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 Zinc with other atoms in the Zn 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:Zn801

b:41.7
occ:1.00
 O A:HOH930 2.0 34.5 1.0
OD2 A:ASP564 2.0 36.7 1.0
NE2 A:HIS563 2.1 33.0 1.0
NE2 A:HIS529 2.2 41.2 1.0
OD1 A:ASP674 2.2 37.2 1.0
O A:HOH946 2.4 41.9 1.0
CD2 A:HIS563 3.0 34.0 1.0
CG A:ASP564 3.0 35.5 1.0
CG A:ASP674 3.1 41.4 1.0
CE1 A:HIS529 3.1 36.4 1.0
CD2 A:HIS529 3.1 38.2 1.0
CE1 A:HIS563 3.2 38.6 1.0
OD2 A:ASP674 3.3 53.3 1.0
OD1 A:ASP564 3.6 34.9 1.0
MG A:MG802 3.7 35.6 1.0
CG A:HIS563 4.2 34.1 1.0
CD2 A:HIS525 4.2 45.7 1.0
CB A:ASP564 4.2 34.9 1.0
O A:HOH968 4.2 32.1 1.0
ND1 A:HIS529 4.2 34.3 1.0
ND1 A:HIS563 4.3 35.2 1.0
CG A:HIS529 4.3 38.0 1.0
O A:HOH936 4.3 51.9 1.0
CB A:ASP674 4.4 41.4 1.0
NE2 A:HIS525 4.5 43.4 1.0
O A:HOH919 4.6 26.6 1.0
CG2 A:VAL533 4.8 28.2 1.0
O A:ASP674 4.9 37.0 1.0
CA A:ASP674 4.9 36.8 1.0

Zinc binding site 2 out of 4 in 5seg

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Zinc 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 Zinc with other atoms in the Zn 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:Zn801

b:41.9
occ:1.00
 NE2 B:HIS563 2.0 34.9 1.0
OD2 B:ASP564 2.1 37.8 1.0
OD1 B:ASP674 2.1 36.5 1.0
O B:HOH935 2.1 27.4 1.0
NE2 B:HIS529 2.1 37.5 1.0
O B:HOH961 2.3 41.7 1.0
CD2 B:HIS563 3.0 31.4 1.0
CG B:ASP674 3.1 34.7 1.0
CG B:ASP564 3.1 31.7 1.0
CE1 B:HIS563 3.1 36.2 1.0
CE1 B:HIS529 3.1 41.9 1.0
CD2 B:HIS529 3.1 36.7 1.0
OD2 B:ASP674 3.3 39.1 1.0
OD1 B:ASP564 3.5 36.9 1.0
MG B:MG802 3.8 30.6 1.0
O B:HOH969 4.0 32.7 1.0
CG B:HIS563 4.1 29.7 1.0
ND1 B:HIS563 4.1 30.9 1.0
CD2 B:HIS525 4.2 42.4 1.0
ND1 B:HIS529 4.2 40.0 1.0
CB B:ASP564 4.2 30.4 1.0
CG B:HIS529 4.3 36.9 1.0
O B:HOH933 4.3 44.7 1.0
CB B:ASP674 4.4 35.3 1.0
NE2 B:HIS525 4.5 41.7 1.0
O B:HOH925 4.6 33.3 1.0
CG2 B:VAL533 4.7 31.3 1.0
CA B:ASP674 4.9 32.7 1.0
O B:ASP674 5.0 40.0 1.0

Zinc binding site 3 out of 4 in 5seg

Go back to Zinc Binding Sites List in 5seg
Zinc 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 Zinc with other atoms in the Zn 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:Zn801

b:41.8
occ:1.00
 O C:HOH954 2.1 47.7 1.0
O C:HOH935 2.1 36.1 1.0
NE2 C:HIS563 2.1 36.5 1.0
NE2 C:HIS529 2.2 39.1 1.0
OD2 C:ASP564 2.2 36.5 1.0
OD1 C:ASP674 2.2 40.0 1.0
CD2 C:HIS563 3.0 34.2 1.0
CG C:ASP674 3.0 42.0 1.0
CD2 C:HIS529 3.1 41.4 1.0
CE1 C:HIS529 3.2 44.0 1.0
CG C:ASP564 3.2 36.2 1.0
CE1 C:HIS563 3.2 39.2 1.0
OD2 C:ASP674 3.3 42.3 1.0
OD1 C:ASP564 3.7 34.9 1.0
MG C:MG802 3.8 36.2 1.0
CD2 C:HIS525 4.1 43.7 1.0
CG C:HIS563 4.2 36.5 1.0
O C:HOH968 4.2 33.7 1.0
ND1 C:HIS529 4.3 37.8 1.0
CG C:HIS529 4.3 38.9 1.0
ND1 C:HIS563 4.3 34.1 1.0
O C:HOH961 4.3 46.5 1.0
CB C:ASP564 4.4 31.4 1.0
CB C:ASP674 4.4 46.1 1.0
NE2 C:HIS525 4.4 43.2 1.0
O C:HOH927 4.6 36.0 1.0
CG2 C:VAL533 4.7 32.4 1.0
O C:HOH975 4.8 63.6 1.0
CA C:ASP674 4.8 46.2 1.0
O C:ASP674 5.0 43.4 1.0

Zinc binding site 4 out of 4 in 5seg

Go back to Zinc Binding Sites List in 5seg
Zinc 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 Zinc with other atoms in the Zn 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:Zn801

b:52.5
occ:1.00
 O D:HOH903 2.0 38.1 1.0
NE2 D:HIS563 2.0 39.0 1.0
OD1 D:ASP674 2.2 47.5 1.0
OD2 D:ASP564 2.2 52.5 1.0
NE2 D:HIS529 2.2 53.3 1.0
O D:HOH917 2.3 43.9 1.0
CD2 D:HIS563 2.9 41.2 1.0
CG D:ASP674 3.1 48.4 1.0
CE1 D:HIS563 3.1 43.3 1.0
CD2 D:HIS529 3.1 60.6 1.0
CG D:ASP564 3.2 40.9 1.0
OD2 D:ASP674 3.3 51.5 1.0
CE1 D:HIS529 3.4 51.5 1.0
OD1 D:ASP564 3.8 49.8 1.0
MG D:MG802 3.9 48.9 1.0
O D:HOH921 4.1 45.6 1.0
CG D:HIS563 4.1 43.9 1.0
ND1 D:HIS563 4.2 42.1 1.0
CB D:ASP564 4.2 45.2 1.0
CD2 D:HIS525 4.2 60.9 1.0
CG D:HIS529 4.3 46.9 1.0
ND1 D:HIS529 4.4 44.9 1.0
CB D:ASP674 4.5 55.3 1.0
O D:HOH901 4.5 44.1 1.0
NE2 D:HIS525 4.6 62.0 1.0
CG2 D:VAL533 4.8 45.6 1.0
O D:ASP674 4.8 52.2 1.0
CA D:ASP674 4.9 48.9 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: Mon Oct 28 04:40:38 2024

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