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Zinc in PDB 5sfh: Crystal Structure of Human Phosphodiesterase 10 in Complex with N- Cyclopropyl-5-[2-(5,8-Dimethyl-[1,2,4]Triazolo[1,5-A]Pyrazin-2-Yl) Ethyl]-N,1-Dimethyl-1,2,4-Triazol-3-Amine

Enzymatic activity of Crystal Structure of Human Phosphodiesterase 10 in Complex with N- Cyclopropyl-5-[2-(5,8-Dimethyl-[1,2,4]Triazolo[1,5-A]Pyrazin-2-Yl) Ethyl]-N,1-Dimethyl-1,2,4-Triazol-3-Amine

All present enzymatic activity of Crystal Structure of Human Phosphodiesterase 10 in Complex with N- Cyclopropyl-5-[2-(5,8-Dimethyl-[1,2,4]Triazolo[1,5-A]Pyrazin-2-Yl) Ethyl]-N,1-Dimethyl-1,2,4-Triazol-3-Amine:
3.1.4.17;

Protein crystallography data

The structure of Crystal Structure of Human Phosphodiesterase 10 in Complex with N- Cyclopropyl-5-[2-(5,8-Dimethyl-[1,2,4]Triazolo[1,5-A]Pyrazin-2-Yl) Ethyl]-N,1-Dimethyl-1,2,4-Triazol-3-Amine, PDB code: 5sfh 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) 43.75 / 2.29
Space group H 3
Cell size a, b, c (Å), α, β, γ (°) 135.463, 135.463, 235.776, 90, 90, 120
R / Rfree (%) 17.4 / 22.1

Other elements in 5sfh:

The structure of Crystal Structure of Human Phosphodiesterase 10 in Complex with N- Cyclopropyl-5-[2-(5,8-Dimethyl-[1,2,4]Triazolo[1,5-A]Pyrazin-2-Yl) Ethyl]-N,1-Dimethyl-1,2,4-Triazol-3-Amine also contains other interesting chemical elements:

Magnesium (Mg) 4 atoms

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of Human Phosphodiesterase 10 in Complex with N- Cyclopropyl-5-[2-(5,8-Dimethyl-[1,2,4]Triazolo[1,5-A]Pyrazin-2-Yl) Ethyl]-N,1-Dimethyl-1,2,4-Triazol-3-Amine (pdb code 5sfh). 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 N- Cyclopropyl-5-[2-(5,8-Dimethyl-[1,2,4]Triazolo[1,5-A]Pyrazin-2-Yl) Ethyl]-N,1-Dimethyl-1,2,4-Triazol-3-Amine, PDB code: 5sfh:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in 5sfh

Go back to Zinc Binding Sites List in 5sfh
Zinc binding site 1 out of 4 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with N- Cyclopropyl-5-[2-(5,8-Dimethyl-[1,2,4]Triazolo[1,5-A]Pyrazin-2-Yl) Ethyl]-N,1-Dimethyl-1,2,4-Triazol-3-Amine


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 N- Cyclopropyl-5-[2-(5,8-Dimethyl-[1,2,4]Triazolo[1,5-A]Pyrazin-2-Yl) Ethyl]-N,1-Dimethyl-1,2,4-Triazol-3-Amine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn801

b:41.9
occ:1.00
 O A:HOH951 2.0 38.2 1.0
OD2 A:ASP564 2.1 43.0 1.0
OD1 A:ASP674 2.1 41.1 1.0
O A:HOH950 2.2 30.8 1.0
NE2 A:HIS529 2.2 36.5 1.0
NE2 A:HIS563 2.2 33.9 1.0
CD2 A:HIS563 3.0 34.8 1.0
CG A:ASP674 3.0 37.6 1.0
CG A:ASP564 3.1 40.0 1.0
CD2 A:HIS529 3.1 32.7 1.0
CE1 A:HIS529 3.2 35.4 1.0
CE1 A:HIS563 3.3 39.4 1.0
OD2 A:ASP674 3.3 44.9 1.0
OD1 A:ASP564 3.6 39.0 1.0
MG A:MG802 3.8 36.0 1.0
CD2 A:HIS525 4.1 45.0 1.0
CG A:HIS563 4.2 36.1 1.0
O A:HOH972 4.2 32.6 1.0
CG A:HIS529 4.3 34.6 1.0
CB A:ASP564 4.3 36.9 1.0
ND1 A:HIS529 4.3 36.9 1.0
ND1 A:HIS563 4.3 36.8 1.0
CB A:ASP674 4.4 37.5 1.0
NE2 A:HIS525 4.5 41.8 1.0
O A:HOH905 4.5 27.0 1.0
CG2 A:VAL533 4.7 30.7 1.0
CA A:ASP674 4.9 36.1 1.0
O A:ASP674 4.9 42.3 1.0

Zinc binding site 2 out of 4 in 5sfh

Go back to Zinc Binding Sites List in 5sfh
Zinc binding site 2 out of 4 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with N- Cyclopropyl-5-[2-(5,8-Dimethyl-[1,2,4]Triazolo[1,5-A]Pyrazin-2-Yl) Ethyl]-N,1-Dimethyl-1,2,4-Triazol-3-Amine


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 N- Cyclopropyl-5-[2-(5,8-Dimethyl-[1,2,4]Triazolo[1,5-A]Pyrazin-2-Yl) Ethyl]-N,1-Dimethyl-1,2,4-Triazol-3-Amine within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn801

b:39.0
occ:1.00
 OD2 B:ASP564 2.1 39.1 1.0
NE2 B:HIS563 2.1 34.6 1.0
OD1 B:ASP674 2.1 35.7 1.0
O B:HOH941 2.1 28.2 1.0
NE2 B:HIS529 2.1 29.7 1.0
O B:HOH921 2.7 46.1 1.0
CD2 B:HIS563 3.0 37.7 1.0
CG B:ASP674 3.1 33.4 1.0
CD2 B:HIS529 3.1 32.5 1.0
CG B:ASP564 3.1 36.9 1.0
CE1 B:HIS563 3.2 36.1 1.0
CE1 B:HIS529 3.2 33.1 1.0
OD2 B:ASP674 3.4 41.8 1.0
OD1 B:ASP564 3.6 35.0 1.0
MG B:MG802 3.8 32.7 1.0
O B:HOH971 4.0 27.2 1.0
CD2 B:HIS525 4.1 37.0 1.0
CG B:HIS563 4.2 34.6 1.0
ND1 B:HIS563 4.2 34.6 1.0
ND1 B:HIS529 4.3 34.1 1.0
CG B:HIS529 4.3 32.0 1.0
CB B:ASP564 4.3 34.0 1.0
CB B:ASP674 4.4 35.8 1.0
O B:HOH926 4.5 48.5 1.0
NE2 B:HIS525 4.5 36.0 1.0
O B:HOH929 4.6 36.5 1.0
CG2 B:VAL533 4.7 31.7 1.0
O B:ASP674 4.8 37.0 1.0
CA B:ASP674 4.8 31.4 1.0

Zinc binding site 3 out of 4 in 5sfh

Go back to Zinc Binding Sites List in 5sfh
Zinc binding site 3 out of 4 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with N- Cyclopropyl-5-[2-(5,8-Dimethyl-[1,2,4]Triazolo[1,5-A]Pyrazin-2-Yl) Ethyl]-N,1-Dimethyl-1,2,4-Triazol-3-Amine


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 N- Cyclopropyl-5-[2-(5,8-Dimethyl-[1,2,4]Triazolo[1,5-A]Pyrazin-2-Yl) Ethyl]-N,1-Dimethyl-1,2,4-Triazol-3-Amine within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn801

b:42.5
occ:1.00
 O C:HOH924 2.0 29.0 1.0
NE2 C:HIS529 2.1 35.2 1.0
OD2 C:ASP564 2.1 38.2 1.0
OD1 C:ASP674 2.2 39.4 1.0
NE2 C:HIS563 2.2 31.3 1.0
O C:HOH929 2.4 49.3 1.0
CG C:ASP674 3.0 34.3 1.0
CD2 C:HIS563 3.1 32.7 1.0
CD2 C:HIS529 3.1 33.0 1.0
CE1 C:HIS529 3.1 33.9 1.0
OD2 C:ASP674 3.2 36.2 1.0
CG C:ASP564 3.2 34.9 1.0
CE1 C:HIS563 3.3 34.5 1.0
OD1 C:ASP564 3.8 36.4 1.0
MG C:MG802 3.8 33.2 1.0
CD2 C:HIS525 4.0 43.1 1.0
O C:HOH969 4.1 33.5 1.0
ND1 C:HIS529 4.2 32.3 1.0
CG C:HIS529 4.2 31.1 1.0
CG C:HIS563 4.3 32.1 1.0
NE2 C:HIS525 4.3 43.2 1.0
CB C:ASP564 4.4 35.8 1.0
ND1 C:HIS563 4.4 32.4 1.0
O C:HOH927 4.4 32.9 1.0
CB C:ASP674 4.4 37.8 1.0
O C:HOH953 4.5 44.5 1.0
CA C:ASP674 4.8 38.3 1.0
CG2 C:VAL533 4.9 33.9 1.0
O C:ASP674 4.9 40.9 1.0

Zinc binding site 4 out of 4 in 5sfh

Go back to Zinc Binding Sites List in 5sfh
Zinc binding site 4 out of 4 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with N- Cyclopropyl-5-[2-(5,8-Dimethyl-[1,2,4]Triazolo[1,5-A]Pyrazin-2-Yl) Ethyl]-N,1-Dimethyl-1,2,4-Triazol-3-Amine


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 N- Cyclopropyl-5-[2-(5,8-Dimethyl-[1,2,4]Triazolo[1,5-A]Pyrazin-2-Yl) Ethyl]-N,1-Dimethyl-1,2,4-Triazol-3-Amine within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn801

b:53.7
occ:1.00
 OD2 D:ASP564 2.1 56.9 1.0
O D:HOH921 2.1 41.4 1.0
NE2 D:HIS563 2.2 46.0 1.0
OD1 D:ASP674 2.3 52.1 1.0
NE2 D:HIS529 2.3 44.4 1.0
O D:HOH904 2.5 43.7 1.0
CD2 D:HIS563 3.0 51.6 1.0
CD2 D:HIS529 3.1 47.2 1.0
CG D:ASP564 3.2 51.3 1.0
CG D:ASP674 3.2 47.1 1.0
CE1 D:HIS563 3.3 53.9 1.0
CE1 D:HIS529 3.4 45.4 1.0
OD2 D:ASP674 3.5 60.0 1.0
OD1 D:ASP564 3.8 51.5 1.0
MG D:MG802 3.8 48.5 1.0
CD2 D:HIS525 4.0 53.0 1.0
O D:HOH920 4.1 41.0 1.0
CG D:HIS563 4.3 51.3 1.0
NE2 D:HIS525 4.3 57.1 1.0
CB D:ASP564 4.3 47.4 1.0
CG D:HIS529 4.3 44.1 1.0
ND1 D:HIS563 4.3 51.1 1.0
ND1 D:HIS529 4.4 46.3 1.0
CB D:ASP674 4.6 50.2 1.0
O D:HOH914 4.7 43.4 1.0
O D:ASP674 4.8 55.0 1.0
CG2 D:VAL533 4.8 48.8 1.0
CA D:ASP674 4.9 51.5 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 04:58:09 2024

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