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Zinc in PDB 5sei: Crystal Structure of Human Phosphodiesterase 10 in Complex with 6- Chloro-2-[(E)-2-(2-Methyl-5-Pyrrolidin-1-Yl-1,2,4-Triazol-3-Yl) Ethenyl]-[1,2,4]Triazolo[1,5-A]Pyridine

Enzymatic activity of Crystal Structure of Human Phosphodiesterase 10 in Complex with 6- Chloro-2-[(E)-2-(2-Methyl-5-Pyrrolidin-1-Yl-1,2,4-Triazol-3-Yl) Ethenyl]-[1,2,4]Triazolo[1,5-A]Pyridine

All present enzymatic activity of Crystal Structure of Human Phosphodiesterase 10 in Complex with 6- Chloro-2-[(E)-2-(2-Methyl-5-Pyrrolidin-1-Yl-1,2,4-Triazol-3-Yl) Ethenyl]-[1,2,4]Triazolo[1,5-A]Pyridine:
3.1.4.17;

Protein crystallography data

The structure of Crystal Structure of Human Phosphodiesterase 10 in Complex with 6- Chloro-2-[(E)-2-(2-Methyl-5-Pyrrolidin-1-Yl-1,2,4-Triazol-3-Yl) Ethenyl]-[1,2,4]Triazolo[1,5-A]Pyridine, PDB code: 5sei was solved by C.Joseph, C.Lerner, 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) 43.50 / 2.37
Space group H 3
Cell size a, b, c (Å), α, β, γ (°) 135.211, 135.211, 235.374, 90, 90, 120
R / Rfree (%) 17.2 / 23.5

Other elements in 5sei:

The structure of Crystal Structure of Human Phosphodiesterase 10 in Complex with 6- Chloro-2-[(E)-2-(2-Methyl-5-Pyrrolidin-1-Yl-1,2,4-Triazol-3-Yl) Ethenyl]-[1,2,4]Triazolo[1,5-A]Pyridine also contains other interesting chemical elements:

Magnesium (Mg) 4 atoms
Chlorine (Cl) 4 atoms

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of Human Phosphodiesterase 10 in Complex with 6- Chloro-2-[(E)-2-(2-Methyl-5-Pyrrolidin-1-Yl-1,2,4-Triazol-3-Yl) Ethenyl]-[1,2,4]Triazolo[1,5-A]Pyridine (pdb code 5sei). 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- Chloro-2-[(E)-2-(2-Methyl-5-Pyrrolidin-1-Yl-1,2,4-Triazol-3-Yl) Ethenyl]-[1,2,4]Triazolo[1,5-A]Pyridine, PDB code: 5sei:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in 5sei

Go back to Zinc Binding Sites List in 5sei
Zinc binding site 1 out of 4 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with 6- Chloro-2-[(E)-2-(2-Methyl-5-Pyrrolidin-1-Yl-1,2,4-Triazol-3-Yl) Ethenyl]-[1,2,4]Triazolo[1,5-A]Pyridine


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- Chloro-2-[(E)-2-(2-Methyl-5-Pyrrolidin-1-Yl-1,2,4-Triazol-3-Yl) Ethenyl]-[1,2,4]Triazolo[1,5-A]Pyridine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn802

b:41.5
occ:1.00
 OD2 A:ASP564 2.1 42.5 1.0
NE2 A:HIS529 2.1 37.1 1.0
O A:HOH938 2.1 33.5 1.0
NE2 A:HIS563 2.2 28.5 1.0
OD1 A:ASP674 2.2 44.2 1.0
O A:HOH914 2.5 34.0 1.0
CD2 A:HIS563 3.0 31.4 1.0
CD2 A:HIS529 3.1 34.6 1.0
CE1 A:HIS529 3.1 35.8 1.0
CG A:ASP564 3.1 37.6 1.0
CG A:ASP674 3.1 40.2 1.0
CE1 A:HIS563 3.3 34.9 1.0
OD2 A:ASP674 3.4 46.4 1.0
OD1 A:ASP564 3.6 40.3 1.0
MG A:MG803 3.8 36.3 1.0
CD2 A:HIS525 4.1 35.8 1.0
O A:HOH948 4.1 42.0 1.0
O A:HOH981 4.2 32.0 1.0
ND1 A:HIS529 4.2 38.5 1.0
CG A:HIS529 4.2 34.7 1.0
CG A:HIS563 4.2 31.7 1.0
CB A:ASP564 4.3 33.8 1.0
NE2 A:HIS525 4.3 38.1 1.0
ND1 A:HIS563 4.3 31.6 1.0
CB A:ASP674 4.5 38.7 1.0
O A:HOH910 4.6 27.4 1.0
CG2 A:VAL533 4.7 30.5 1.0
O A:ASP674 4.8 38.0 1.0
CA A:ASP674 4.9 36.4 1.0

Zinc binding site 2 out of 4 in 5sei

Go back to Zinc Binding Sites List in 5sei
Zinc binding site 2 out of 4 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with 6- Chloro-2-[(E)-2-(2-Methyl-5-Pyrrolidin-1-Yl-1,2,4-Triazol-3-Yl) Ethenyl]-[1,2,4]Triazolo[1,5-A]Pyridine


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- Chloro-2-[(E)-2-(2-Methyl-5-Pyrrolidin-1-Yl-1,2,4-Triazol-3-Yl) Ethenyl]-[1,2,4]Triazolo[1,5-A]Pyridine within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn802

b:39.9
occ:1.00
 O B:HOH964 2.1 33.9 1.0
NE2 B:HIS563 2.1 30.8 1.0
NE2 B:HIS529 2.1 31.3 1.0
OD2 B:ASP564 2.1 37.9 1.0
OD1 B:ASP674 2.2 35.7 1.0
CD2 B:HIS563 3.0 34.3 1.0
CD2 B:HIS529 3.1 32.2 1.0
CG B:ASP674 3.1 34.2 1.0
CG B:ASP564 3.2 33.9 1.0
CE1 B:HIS529 3.2 31.4 1.0
CE1 B:HIS563 3.2 34.7 1.0
OD2 B:ASP674 3.4 37.6 1.0
OD1 B:ASP564 3.6 32.4 1.0
MG B:MG803 3.7 30.5 1.0
O B:HOH959 4.0 27.7 1.0
CD2 B:HIS525 4.1 37.6 1.0
CG B:HIS563 4.2 30.9 1.0
ND1 B:HIS529 4.2 36.0 1.0
CG B:HIS529 4.3 32.2 1.0
O B:HOH941 4.3 33.1 1.0
ND1 B:HIS563 4.3 31.9 1.0
CB B:ASP564 4.4 32.5 1.0
NE2 B:HIS525 4.4 34.4 1.0
CB B:ASP674 4.5 36.0 1.0
O B:HOH943 4.7 35.0 1.0
CG2 B:VAL533 4.8 28.4 1.0
O B:ASP674 4.8 39.4 1.0
CA B:ASP674 4.9 35.8 1.0

Zinc binding site 3 out of 4 in 5sei

Go back to Zinc Binding Sites List in 5sei
Zinc binding site 3 out of 4 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with 6- Chloro-2-[(E)-2-(2-Methyl-5-Pyrrolidin-1-Yl-1,2,4-Triazol-3-Yl) Ethenyl]-[1,2,4]Triazolo[1,5-A]Pyridine


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- Chloro-2-[(E)-2-(2-Methyl-5-Pyrrolidin-1-Yl-1,2,4-Triazol-3-Yl) Ethenyl]-[1,2,4]Triazolo[1,5-A]Pyridine within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn802

b:40.5
occ:1.00
 OD2 C:ASP564 2.1 34.7 1.0
NE2 C:HIS529 2.1 37.0 1.0
O C:HOH949 2.1 24.9 1.0
NE2 C:HIS563 2.2 34.5 1.0
OD1 C:ASP674 2.2 41.1 1.0
O C:HOH908 2.6 39.8 1.0
CD2 C:HIS529 3.1 34.4 1.0
CD2 C:HIS563 3.1 34.2 1.0
CG C:ASP674 3.1 36.6 1.0
CE1 C:HIS529 3.1 35.4 1.0
CG C:ASP564 3.2 34.1 1.0
CE1 C:HIS563 3.2 35.9 1.0
OD2 C:ASP674 3.4 36.6 1.0
OD1 C:ASP564 3.8 36.4 1.0
MG C:MG803 3.8 31.2 1.0
CD2 C:HIS525 4.0 36.1 1.0
ND1 C:HIS529 4.2 35.8 1.0
CG C:HIS529 4.2 33.8 1.0
NE2 C:HIS525 4.2 36.7 1.0
CG C:HIS563 4.2 33.0 1.0
ND1 C:HIS563 4.3 32.6 1.0
CB C:ASP564 4.3 33.6 1.0
O C:HOH987 4.4 33.2 1.0
O C:HOH966 4.4 43.1 1.0
O C:HOH976 4.4 44.9 1.0
CB C:ASP674 4.5 38.8 1.0
O C:HOH936 4.5 34.6 1.0
CG2 C:VAL533 4.8 35.3 1.0
CA C:ASP674 4.9 39.6 1.0
O C:ASP674 4.9 41.0 1.0

Zinc binding site 4 out of 4 in 5sei

Go back to Zinc Binding Sites List in 5sei
Zinc binding site 4 out of 4 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with 6- Chloro-2-[(E)-2-(2-Methyl-5-Pyrrolidin-1-Yl-1,2,4-Triazol-3-Yl) Ethenyl]-[1,2,4]Triazolo[1,5-A]Pyridine


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- Chloro-2-[(E)-2-(2-Methyl-5-Pyrrolidin-1-Yl-1,2,4-Triazol-3-Yl) Ethenyl]-[1,2,4]Triazolo[1,5-A]Pyridine within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn802

b:57.0
occ:1.00
 O D:HOH928 2.1 41.1 1.0
OD2 D:ASP564 2.1 63.4 1.0
NE2 D:HIS563 2.1 43.3 1.0
O D:HOH915 2.3 58.9 1.0
NE2 D:HIS529 2.3 48.4 1.0
OD1 D:ASP674 2.4 54.1 1.0
CD2 D:HIS563 3.0 49.1 1.0
CG D:ASP564 3.1 53.0 1.0
CD2 D:HIS529 3.2 51.9 1.0
CG D:ASP674 3.2 52.3 1.0
CE1 D:HIS563 3.2 46.8 1.0
CE1 D:HIS529 3.3 47.6 1.0
OD2 D:ASP674 3.4 55.8 1.0
OD1 D:ASP564 3.7 46.5 1.0
MG D:MG803 3.8 52.5 1.0
O D:HOH926 4.0 47.4 1.0
CD2 D:HIS525 4.1 62.1 1.0
CG D:HIS563 4.2 48.2 1.0
CB D:ASP564 4.3 51.1 1.0
ND1 D:HIS563 4.3 44.7 1.0
O D:HOH921 4.4 59.2 1.0
CG D:HIS529 4.4 49.0 1.0
NE2 D:HIS525 4.4 60.6 1.0
ND1 D:HIS529 4.4 49.7 1.0
CB D:ASP674 4.5 56.4 1.0
O D:HOH902 4.8 44.3 1.0
CG2 D:VAL533 4.8 50.4 1.0
O D:ASP674 4.9 62.9 1.0
CA D:ASP674 4.9 54.7 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: Fri Apr 7 21:44:23 2023

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