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Zinc in PDB 5sey: Crystal Structure of Human Phosphodiesterase 10 in Complex with [2- Cyclopropyl-6-[2-(1-Methyl-4-Phenylimidazol-2-Yl)Ethynyl]Imidazo[1,2- B]Pyridazin-3-Yl]Methanol

Enzymatic activity of Crystal Structure of Human Phosphodiesterase 10 in Complex with [2- Cyclopropyl-6-[2-(1-Methyl-4-Phenylimidazol-2-Yl)Ethynyl]Imidazo[1,2- B]Pyridazin-3-Yl]Methanol

All present enzymatic activity of Crystal Structure of Human Phosphodiesterase 10 in Complex with [2- Cyclopropyl-6-[2-(1-Methyl-4-Phenylimidazol-2-Yl)Ethynyl]Imidazo[1,2- B]Pyridazin-3-Yl]Methanol:
3.1.4.17;

Protein crystallography data

The structure of Crystal Structure of Human Phosphodiesterase 10 in Complex with [2- Cyclopropyl-6-[2-(1-Methyl-4-Phenylimidazol-2-Yl)Ethynyl]Imidazo[1,2- B]Pyridazin-3-Yl]Methanol, PDB code: 5sey was solved by C.Joseph, K.Groebke-Zbinden, 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) 43.70 / 2.29
Space group H 3
Cell size a, b, c (Å), α, β, γ (°) 135.139, 135.139, 235.509, 90, 90, 120
R / Rfree (%) 17.3 / 23.4

Other elements in 5sey:

The structure of Crystal Structure of Human Phosphodiesterase 10 in Complex with [2- Cyclopropyl-6-[2-(1-Methyl-4-Phenylimidazol-2-Yl)Ethynyl]Imidazo[1,2- B]Pyridazin-3-Yl]Methanol 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 [2- Cyclopropyl-6-[2-(1-Methyl-4-Phenylimidazol-2-Yl)Ethynyl]Imidazo[1,2- B]Pyridazin-3-Yl]Methanol (pdb code 5sey). 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- Cyclopropyl-6-[2-(1-Methyl-4-Phenylimidazol-2-Yl)Ethynyl]Imidazo[1,2- B]Pyridazin-3-Yl]Methanol, PDB code: 5sey:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in 5sey

Go back to Zinc Binding Sites List in 5sey
Zinc binding site 1 out of 4 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with [2- Cyclopropyl-6-[2-(1-Methyl-4-Phenylimidazol-2-Yl)Ethynyl]Imidazo[1,2- B]Pyridazin-3-Yl]Methanol


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- Cyclopropyl-6-[2-(1-Methyl-4-Phenylimidazol-2-Yl)Ethynyl]Imidazo[1,2- B]Pyridazin-3-Yl]Methanol within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn801

b:40.8
occ:1.00
 NE2 A:HIS563 2.1 32.1 1.0
NE2 A:HIS529 2.1 43.2 1.0
OD1 A:ASP674 2.1 40.5 1.0
OD2 A:ASP564 2.1 35.3 1.0
O A:HOH944 2.2 28.2 1.0
O A:HOH945 2.4 36.0 1.0
CD2 A:HIS563 2.9 35.5 1.0
CG A:ASP674 3.0 37.8 1.0
CE1 A:HIS529 3.1 37.5 1.0
CG A:ASP564 3.1 32.5 1.0
CD2 A:HIS529 3.2 37.9 1.0
CE1 A:HIS563 3.2 39.5 1.0
OD2 A:ASP674 3.2 38.9 1.0
OD1 A:ASP564 3.6 29.1 1.0
MG A:MG802 3.8 34.3 1.0
O A:HOH961 4.1 29.5 1.0
CD2 A:HIS525 4.1 36.7 1.0
CG A:HIS563 4.1 34.7 1.0
O A:HOH949 4.2 39.4 1.0
ND1 A:HIS529 4.2 38.9 1.0
ND1 A:HIS563 4.3 31.3 1.0
CB A:ASP564 4.3 31.8 1.0
CG A:HIS529 4.3 36.7 1.0
CB A:ASP674 4.4 38.9 1.0
NE2 A:HIS525 4.4 38.7 1.0
O A:HOH904 4.6 27.9 1.0
CG2 A:VAL533 4.8 28.8 1.0
O A:ASP674 4.8 38.1 1.0
CA A:ASP674 4.9 37.1 1.0
O A:HOH916 5.0 28.7 1.0

Zinc binding site 2 out of 4 in 5sey

Go back to Zinc Binding Sites List in 5sey
Zinc binding site 2 out of 4 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with [2- Cyclopropyl-6-[2-(1-Methyl-4-Phenylimidazol-2-Yl)Ethynyl]Imidazo[1,2- B]Pyridazin-3-Yl]Methanol


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- Cyclopropyl-6-[2-(1-Methyl-4-Phenylimidazol-2-Yl)Ethynyl]Imidazo[1,2- B]Pyridazin-3-Yl]Methanol within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn801

b:40.0
occ:1.00
 OD2 B:ASP564 2.1 34.2 1.0
NE2 B:HIS563 2.1 34.6 1.0
NE2 B:HIS529 2.2 31.4 1.0
O B:HOH941 2.2 28.3 1.0
OD1 B:ASP674 2.2 38.1 1.0
O B:HOH969 2.4 40.1 1.0
CG B:ASP674 3.0 33.1 1.0
CD2 B:HIS563 3.0 35.2 1.0
CD2 B:HIS529 3.1 31.1 1.0
CG B:ASP564 3.1 30.2 1.0
CE1 B:HIS563 3.2 36.2 1.0
CE1 B:HIS529 3.2 34.2 1.0
OD2 B:ASP674 3.2 37.3 1.0
OD1 B:ASP564 3.6 29.4 1.0
MG B:MG802 3.8 33.4 1.0
O B:HOH960 3.9 26.5 1.0
O B:HOH954 4.1 36.4 1.0
CD2 B:HIS525 4.1 42.1 1.0
CG B:HIS563 4.2 31.4 1.0
O B:HOH979 4.2 55.5 1.0
ND1 B:HIS563 4.3 32.3 1.0
CG B:HIS529 4.3 31.0 1.0
ND1 B:HIS529 4.3 31.3 1.0
CB B:ASP564 4.3 31.6 1.0
CB B:ASP674 4.4 33.5 1.0
NE2 B:HIS525 4.5 43.0 1.0
O B:HOH930 4.6 31.9 1.0
CG2 B:VAL533 4.7 33.2 1.0
CA B:ASP674 4.9 31.7 1.0
O B:ASP674 4.9 35.3 1.0

Zinc binding site 3 out of 4 in 5sey

Go back to Zinc Binding Sites List in 5sey
Zinc binding site 3 out of 4 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with [2- Cyclopropyl-6-[2-(1-Methyl-4-Phenylimidazol-2-Yl)Ethynyl]Imidazo[1,2- B]Pyridazin-3-Yl]Methanol


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- Cyclopropyl-6-[2-(1-Methyl-4-Phenylimidazol-2-Yl)Ethynyl]Imidazo[1,2- B]Pyridazin-3-Yl]Methanol within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn801

b:41.0
occ:1.00
 O C:HOH925 2.0 27.4 1.0
OD2 C:ASP564 2.1 39.0 1.0
NE2 C:HIS529 2.1 39.6 1.0
OD1 C:ASP674 2.2 40.8 1.0
NE2 C:HIS563 2.2 34.0 1.0
O C:HOH944 2.5 44.7 1.0
CG C:ASP674 3.1 35.1 1.0
CD2 C:HIS563 3.1 29.8 1.0
CE1 C:HIS529 3.1 35.0 1.0
CD2 C:HIS529 3.2 36.3 1.0
CG C:ASP564 3.2 34.9 1.0
OD2 C:ASP674 3.3 36.6 1.0
CE1 C:HIS563 3.3 32.2 1.0
OD1 C:ASP564 3.7 35.9 1.0
MG C:MG802 3.7 34.9 1.0
O C:HOH938 4.1 43.9 1.0
CD2 C:HIS525 4.1 37.6 1.0
ND1 C:HIS529 4.2 35.5 1.0
CG C:HIS563 4.3 29.0 1.0
CG C:HIS529 4.3 34.0 1.0
O C:HOH968 4.3 33.9 1.0
ND1 C:HIS563 4.4 28.9 1.0
CB C:ASP564 4.4 32.2 1.0
NE2 C:HIS525 4.4 34.8 1.0
CB C:ASP674 4.4 35.2 1.0
O C:HOH927 4.6 33.7 1.0
O C:HOH973 4.8 42.5 1.0
CG2 C:VAL533 4.8 34.6 1.0
CA C:ASP674 4.8 37.6 1.0
O C:ASP674 4.9 39.2 1.0
O C:HOH933 4.9 34.7 1.0

Zinc binding site 4 out of 4 in 5sey

Go back to Zinc Binding Sites List in 5sey
Zinc binding site 4 out of 4 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with [2- Cyclopropyl-6-[2-(1-Methyl-4-Phenylimidazol-2-Yl)Ethynyl]Imidazo[1,2- B]Pyridazin-3-Yl]Methanol


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- Cyclopropyl-6-[2-(1-Methyl-4-Phenylimidazol-2-Yl)Ethynyl]Imidazo[1,2- B]Pyridazin-3-Yl]Methanol within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn801

b:56.0
occ:1.00
 NE2 D:HIS563 2.1 45.6 1.0
OD2 D:ASP564 2.2 66.7 1.0
O D:HOH919 2.2 34.1 1.0
NE2 D:HIS529 2.3 48.1 1.0
O D:HOH912 2.3 45.6 1.0
OD1 D:ASP674 2.3 62.3 1.0
CD2 D:HIS563 3.0 48.1 1.0
CG D:ASP674 3.2 55.5 1.0
CG D:ASP564 3.2 53.6 1.0
CD2 D:HIS529 3.2 53.1 1.0
CE1 D:HIS563 3.3 48.3 1.0
CE1 D:HIS529 3.3 49.6 1.0
OD2 D:ASP674 3.5 59.1 1.0
MG D:MG802 3.7 52.9 1.0
OD1 D:ASP564 3.8 56.1 1.0
O D:HOH909 3.8 53.0 1.0
O D:HOH920 4.0 48.1 1.0
CD2 D:HIS525 4.2 61.9 1.0
CG D:HIS563 4.2 53.9 1.0
CB D:ASP564 4.2 49.4 1.0
ND1 D:HIS563 4.3 49.7 1.0
CG D:HIS529 4.4 46.5 1.0
ND1 D:HIS529 4.4 48.7 1.0
NE2 D:HIS525 4.5 61.5 1.0
CB D:ASP674 4.5 63.8 1.0
O D:HOH905 4.6 46.8 1.0
CG2 D:VAL533 4.8 54.9 1.0
O D:ASP674 4.9 65.6 1.0
CA D:ASP674 4.9 59.4 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 04:47:48 2024

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