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Zinc in PDB 5se3: Crystal Structure of Human Phosphodiesterase 10 in Complex with 2- Chloro-N-(2-Phenyl-[1,2,4]Triazolo[1,5-A]Pyridin-7-Yl)Pyridine-4- Carboxamide

Enzymatic activity of Crystal Structure of Human Phosphodiesterase 10 in Complex with 2- Chloro-N-(2-Phenyl-[1,2,4]Triazolo[1,5-A]Pyridin-7-Yl)Pyridine-4- Carboxamide

All present enzymatic activity of Crystal Structure of Human Phosphodiesterase 10 in Complex with 2- Chloro-N-(2-Phenyl-[1,2,4]Triazolo[1,5-A]Pyridin-7-Yl)Pyridine-4- Carboxamide:
3.1.4.17;

Protein crystallography data

The structure of Crystal Structure of Human Phosphodiesterase 10 in Complex with 2- Chloro-N-(2-Phenyl-[1,2,4]Triazolo[1,5-A]Pyridin-7-Yl)Pyridine-4- Carboxamide, PDB code: 5se3 was solved by C.Joseph, A.Flohr, 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) 43.54 / 2.14
Space group H 3
Cell size a, b, c (Å), α, β, γ (°) 135.37, 135.37, 235.253, 90, 90, 120
R / Rfree (%) 18 / 22.6

Other elements in 5se3:

The structure of Crystal Structure of Human Phosphodiesterase 10 in Complex with 2- Chloro-N-(2-Phenyl-[1,2,4]Triazolo[1,5-A]Pyridin-7-Yl)Pyridine-4- Carboxamide 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 2- Chloro-N-(2-Phenyl-[1,2,4]Triazolo[1,5-A]Pyridin-7-Yl)Pyridine-4- Carboxamide (pdb code 5se3). 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 2- Chloro-N-(2-Phenyl-[1,2,4]Triazolo[1,5-A]Pyridin-7-Yl)Pyridine-4- Carboxamide, PDB code: 5se3:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in 5se3

Go back to Zinc Binding Sites List in 5se3
Zinc binding site 1 out of 4 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with 2- Chloro-N-(2-Phenyl-[1,2,4]Triazolo[1,5-A]Pyridin-7-Yl)Pyridine-4- 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 2- Chloro-N-(2-Phenyl-[1,2,4]Triazolo[1,5-A]Pyridin-7-Yl)Pyridine-4- Carboxamide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn801

b:31.6
occ:1.00
 OD2 A:ASP564 2.1 25.7 1.0
NE2 A:HIS563 2.1 28.9 1.0
NE2 A:HIS529 2.1 31.7 1.0
OD1 A:ASP674 2.1 27.9 1.0
O A:HOH937 2.1 26.9 1.0
O A:HOH964 2.4 37.0 1.0
CD2 A:HIS563 2.9 25.3 1.0
CG A:ASP674 3.0 31.3 1.0
CE1 A:HIS529 3.1 29.7 1.0
CG A:ASP564 3.1 23.9 1.0
CD2 A:HIS529 3.1 28.4 1.0
CE1 A:HIS563 3.2 31.3 1.0
OD2 A:ASP674 3.3 36.1 1.0
OD1 A:ASP564 3.7 25.3 1.0
MG A:MG802 3.8 26.9 1.0
CG A:HIS563 4.1 28.0 1.0
O A:HOH1006 4.2 23.8 1.0
CD2 A:HIS525 4.2 28.5 1.0
ND1 A:HIS529 4.2 27.9 1.0
ND1 A:HIS563 4.2 28.1 1.0
CG A:HIS529 4.2 27.8 1.0
CB A:ASP564 4.3 23.5 1.0
O A:HOH941 4.3 30.1 1.0
CB A:ASP674 4.4 28.7 1.0
O A:HOH1017 4.5 48.6 1.0
NE2 A:HIS525 4.5 29.0 1.0
O A:HOH950 4.6 24.4 1.0
CG2 A:VAL533 4.7 25.0 1.0
O A:ASP674 4.7 28.6 1.0
CA A:ASP674 4.8 27.4 1.0

Zinc binding site 2 out of 4 in 5se3

Go back to Zinc Binding Sites List in 5se3
Zinc binding site 2 out of 4 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with 2- Chloro-N-(2-Phenyl-[1,2,4]Triazolo[1,5-A]Pyridin-7-Yl)Pyridine-4- 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 2- Chloro-N-(2-Phenyl-[1,2,4]Triazolo[1,5-A]Pyridin-7-Yl)Pyridine-4- Carboxamide within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn801

b:30.7
occ:1.00
 NE2 B:HIS563 2.1 22.7 1.0
OD2 B:ASP564 2.1 24.6 1.0
O B:HOH964 2.1 18.9 1.0
OD1 B:ASP674 2.1 27.2 1.0
NE2 B:HIS529 2.1 25.5 1.0
O B:HOH982 2.2 31.6 1.0
CG B:ASP674 3.0 27.8 1.0
CD2 B:HIS563 3.0 24.5 1.0
CE1 B:HIS563 3.1 25.5 1.0
CD2 B:HIS529 3.1 26.2 1.0
CG B:ASP564 3.1 24.7 1.0
CE1 B:HIS529 3.2 28.7 1.0
OD2 B:ASP674 3.2 27.2 1.0
OD1 B:ASP564 3.6 24.9 1.0
MG B:MG802 3.8 24.9 1.0
O B:HOH1012 4.1 22.1 1.0
CD2 B:HIS525 4.1 27.9 1.0
O B:HOH987 4.1 31.9 1.0
CG B:HIS563 4.2 27.1 1.0
ND1 B:HIS563 4.2 24.5 1.0
CG B:HIS529 4.2 25.8 1.0
ND1 B:HIS529 4.3 27.6 1.0
CB B:ASP564 4.3 23.4 1.0
NE2 B:HIS525 4.4 26.9 1.0
CB B:ASP674 4.4 25.5 1.0
O B:HOH947 4.6 24.0 1.0
CG2 B:VAL533 4.7 27.8 1.0
CA B:ASP674 4.8 24.4 1.0
O B:ASP674 4.8 23.5 1.0

Zinc binding site 3 out of 4 in 5se3

Go back to Zinc Binding Sites List in 5se3
Zinc binding site 3 out of 4 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with 2- Chloro-N-(2-Phenyl-[1,2,4]Triazolo[1,5-A]Pyridin-7-Yl)Pyridine-4- 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 2- Chloro-N-(2-Phenyl-[1,2,4]Triazolo[1,5-A]Pyridin-7-Yl)Pyridine-4- Carboxamide within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn801

b:32.6
occ:1.00
 O C:HOH983 2.1 23.3 1.0
OD1 C:ASP674 2.1 27.6 1.0
NE2 C:HIS529 2.2 27.3 1.0
OD2 C:ASP564 2.2 29.1 1.0
NE2 C:HIS563 2.2 27.3 1.0
O C:HOH1008 2.2 31.8 1.0
CD2 C:HIS563 3.0 24.9 1.0
CG C:ASP674 3.0 30.6 1.0
CE1 C:HIS529 3.1 29.9 1.0
CD2 C:HIS529 3.1 28.9 1.0
CG C:ASP564 3.1 28.1 1.0
CE1 C:HIS563 3.3 28.6 1.0
OD2 C:ASP674 3.3 32.6 1.0
OD1 C:ASP564 3.6 26.8 1.0
MG C:MG802 3.9 27.6 1.0
CD2 C:HIS525 4.1 33.8 1.0
O C:HOH1019 4.2 23.9 1.0
CG C:HIS563 4.2 28.0 1.0
ND1 C:HIS529 4.2 26.2 1.0
CG C:HIS529 4.3 28.4 1.0
ND1 C:HIS563 4.3 25.4 1.0
O C:HOH970 4.3 36.9 1.0
CB C:ASP564 4.3 24.8 1.0
NE2 C:HIS525 4.4 35.4 1.0
CB C:ASP674 4.4 30.4 1.0
O C:HOH953 4.6 30.1 1.0
CG2 C:VAL533 4.8 26.7 1.0
CA C:ASP674 4.8 31.3 1.0
O C:ASP674 4.8 29.3 1.0

Zinc binding site 4 out of 4 in 5se3

Go back to Zinc Binding Sites List in 5se3
Zinc binding site 4 out of 4 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with 2- Chloro-N-(2-Phenyl-[1,2,4]Triazolo[1,5-A]Pyridin-7-Yl)Pyridine-4- 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 2- Chloro-N-(2-Phenyl-[1,2,4]Triazolo[1,5-A]Pyridin-7-Yl)Pyridine-4- Carboxamide within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn801

b:40.6
occ:1.00
 O D:HOH923 2.1 25.3 1.0
NE2 D:HIS563 2.1 30.5 1.0
OD2 D:ASP564 2.2 46.3 1.0
NE2 D:HIS529 2.2 38.0 1.0
O D:HOH960 2.2 38.7 1.0
OD1 D:ASP674 2.2 35.5 1.0
CD2 D:HIS563 2.9 29.6 1.0
CG D:ASP674 3.1 37.5 1.0
CG D:ASP564 3.1 34.1 1.0
CD2 D:HIS529 3.2 43.6 1.0
CE1 D:HIS529 3.2 40.0 1.0
OD2 D:ASP674 3.3 33.2 1.0
CE1 D:HIS563 3.3 31.7 1.0
OD1 D:ASP564 3.6 35.4 1.0
MG D:MG802 3.8 38.1 1.0
O D:HOH946 4.1 32.9 1.0
CG D:HIS563 4.1 30.6 1.0
O D:HOH912 4.1 42.4 1.0
CD2 D:HIS525 4.2 38.8 1.0
CB D:ASP564 4.2 37.4 1.0
ND1 D:HIS563 4.3 33.5 1.0
ND1 D:HIS529 4.3 41.2 1.0
CG D:HIS529 4.3 36.5 1.0
CB D:ASP674 4.4 39.4 1.0
NE2 D:HIS525 4.5 40.0 1.0
O D:HOH909 4.6 35.5 1.0
CG2 D:VAL533 4.7 39.1 1.0
O D:ASP674 4.7 37.1 1.0
CA D:ASP674 4.8 36.6 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 04:34:57 2024

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