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Zinc in PDB 5sf1: Crystal Structure of Human Phosphodiesterase 10 in Complex with 2- (Difluoromethyl)-3-Methyl-6-[2-(1-Methyl-4-Phenylimidazol-2-Yl) Ethynyl]Imidazo[1,2-B]Pyridazine

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

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

Protein crystallography data

The structure of Crystal Structure of Human Phosphodiesterase 10 in Complex with 2- (Difluoromethyl)-3-Methyl-6-[2-(1-Methyl-4-Phenylimidazol-2-Yl) Ethynyl]Imidazo[1,2-B]Pyridazine, PDB code: 5sf1 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) 43.74 / 2.11
Space group H 3
Cell size a, b, c (Å), α, β, γ (°) 135.436, 135.436, 235.715, 90, 90, 120
R / Rfree (%) 18.4 / 23.1

Other elements in 5sf1:

The structure of Crystal Structure of Human Phosphodiesterase 10 in Complex with 2- (Difluoromethyl)-3-Methyl-6-[2-(1-Methyl-4-Phenylimidazol-2-Yl) Ethynyl]Imidazo[1,2-B]Pyridazine also contains other interesting chemical elements:

Magnesium (Mg) 4 atoms
Fluorine (F) 8 atoms

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of Human Phosphodiesterase 10 in Complex with 2- (Difluoromethyl)-3-Methyl-6-[2-(1-Methyl-4-Phenylimidazol-2-Yl) Ethynyl]Imidazo[1,2-B]Pyridazine (pdb code 5sf1). 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- (Difluoromethyl)-3-Methyl-6-[2-(1-Methyl-4-Phenylimidazol-2-Yl) Ethynyl]Imidazo[1,2-B]Pyridazine, PDB code: 5sf1:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in 5sf1

Go back to Zinc Binding Sites List in 5sf1
Zinc binding site 1 out of 4 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with 2- (Difluoromethyl)-3-Methyl-6-[2-(1-Methyl-4-Phenylimidazol-2-Yl) Ethynyl]Imidazo[1,2-B]Pyridazine


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- (Difluoromethyl)-3-Methyl-6-[2-(1-Methyl-4-Phenylimidazol-2-Yl) Ethynyl]Imidazo[1,2-B]Pyridazine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn802

b:36.1
occ:1.00
 O A:HOH958 2.2 28.9 1.0
NE2 A:HIS563 2.2 30.3 1.0
OD2 A:ASP564 2.2 31.4 1.0
OD1 A:ASP674 2.2 33.9 1.0
O A:HOH961 2.2 31.3 1.0
NE2 A:HIS529 2.2 32.1 1.0
CD2 A:HIS563 3.0 32.3 1.0
CG A:ASP674 3.1 34.0 1.0
CG A:ASP564 3.1 30.2 1.0
CD2 A:HIS529 3.2 30.7 1.0
CE1 A:HIS529 3.2 32.2 1.0
CE1 A:HIS563 3.3 34.4 1.0
OD2 A:ASP674 3.3 35.9 1.0
OD1 A:ASP564 3.6 28.5 1.0
MG A:MG803 3.8 28.6 1.0
O A:HOH967 4.0 25.1 1.0
CG A:HIS563 4.2 31.6 1.0
CD2 A:HIS525 4.2 31.6 1.0
O A:HOH945 4.3 37.3 1.0
ND1 A:HIS529 4.3 32.5 1.0
ND1 A:HIS563 4.3 31.0 1.0
CG A:HIS529 4.3 31.6 1.0
CB A:ASP564 4.4 29.3 1.0
CB A:ASP674 4.4 33.1 1.0
NE2 A:HIS525 4.5 35.0 1.0
O A:HOH910 4.6 26.6 1.0
CG2 A:VAL533 4.8 32.1 1.0
CA A:ASP674 4.9 30.4 1.0
O A:ASP674 4.9 33.8 1.0

Zinc binding site 2 out of 4 in 5sf1

Go back to Zinc Binding Sites List in 5sf1
Zinc binding site 2 out of 4 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with 2- (Difluoromethyl)-3-Methyl-6-[2-(1-Methyl-4-Phenylimidazol-2-Yl) Ethynyl]Imidazo[1,2-B]Pyridazine


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- (Difluoromethyl)-3-Methyl-6-[2-(1-Methyl-4-Phenylimidazol-2-Yl) Ethynyl]Imidazo[1,2-B]Pyridazine within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn802

b:34.5
occ:1.00
 OD1 B:ASP674 2.1 27.9 1.0
NE2 B:HIS563 2.1 29.0 1.0
O B:HOH944 2.2 24.9 1.0
OD2 B:ASP564 2.2 29.3 1.0
NE2 B:HIS529 2.2 27.8 1.0
O B:HOH950 2.3 37.7 1.0
CG B:ASP674 3.0 28.6 1.0
CD2 B:HIS563 3.0 27.4 1.0
CD2 B:HIS529 3.1 31.7 1.0
CG B:ASP564 3.1 29.0 1.0
OD2 B:ASP674 3.2 31.7 1.0
CE1 B:HIS563 3.2 29.6 1.0
CE1 B:HIS529 3.3 30.9 1.0
OD1 B:ASP564 3.6 29.6 1.0
MG B:MG803 3.9 33.2 1.0
O B:HOH951 3.9 26.6 1.0
O B:HOH933 4.0 36.6 1.0
CD2 B:HIS525 4.1 27.9 1.0
CG B:HIS563 4.2 27.4 1.0
ND1 B:HIS563 4.3 28.8 1.0
CG B:HIS529 4.3 29.3 1.0
O B:HOH986 4.3 48.9 1.0
ND1 B:HIS529 4.4 27.0 1.0
CB B:ASP564 4.4 27.8 1.0
NE2 B:HIS525 4.4 32.5 1.0
CB B:ASP674 4.4 28.5 1.0
O B:HOH924 4.6 31.2 1.0
CG2 B:VAL533 4.7 27.1 1.0
CA B:ASP674 4.9 26.6 1.0
O B:ASP674 4.9 28.4 1.0

Zinc binding site 3 out of 4 in 5sf1

Go back to Zinc Binding Sites List in 5sf1
Zinc binding site 3 out of 4 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with 2- (Difluoromethyl)-3-Methyl-6-[2-(1-Methyl-4-Phenylimidazol-2-Yl) Ethynyl]Imidazo[1,2-B]Pyridazine


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- (Difluoromethyl)-3-Methyl-6-[2-(1-Methyl-4-Phenylimidazol-2-Yl) Ethynyl]Imidazo[1,2-B]Pyridazine within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn802

b:35.6
occ:1.00
 O C:HOH915 2.1 28.9 1.0
OD2 C:ASP564 2.1 29.8 1.0
NE2 C:HIS529 2.2 33.6 1.0
O C:HOH962 2.2 36.5 1.0
OD1 C:ASP674 2.2 28.4 1.0
NE2 C:HIS563 2.3 29.8 1.0
CD2 C:HIS563 3.0 27.1 1.0
CG C:ASP674 3.0 31.6 1.0
CD2 C:HIS529 3.1 32.4 1.0
CG C:ASP564 3.2 30.5 1.0
OD2 C:ASP674 3.2 35.1 1.0
CE1 C:HIS529 3.2 36.8 1.0
CE1 C:HIS563 3.4 30.7 1.0
OD1 C:ASP564 3.7 32.2 1.0
MG C:MG803 3.7 31.2 1.0
O C:HOH932 4.1 36.3 1.0
CD2 C:HIS525 4.1 35.3 1.0
O C:HOH971 4.2 28.0 1.0
CG C:HIS563 4.2 29.6 1.0
CG C:HIS529 4.3 31.5 1.0
CB C:ASP564 4.3 27.6 1.0
ND1 C:HIS529 4.3 32.0 1.0
ND1 C:HIS563 4.4 28.5 1.0
NE2 C:HIS525 4.4 35.1 1.0
CB C:ASP674 4.4 28.4 1.0
O C:HOH983 4.5 46.9 1.0
O C:HOH931 4.6 28.3 1.0
CG2 C:VAL533 4.8 33.5 1.0
CA C:ASP674 4.8 29.3 1.0
O C:ASP674 4.9 29.5 1.0

Zinc binding site 4 out of 4 in 5sf1

Go back to Zinc Binding Sites List in 5sf1
Zinc binding site 4 out of 4 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with 2- (Difluoromethyl)-3-Methyl-6-[2-(1-Methyl-4-Phenylimidazol-2-Yl) Ethynyl]Imidazo[1,2-B]Pyridazine


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- (Difluoromethyl)-3-Methyl-6-[2-(1-Methyl-4-Phenylimidazol-2-Yl) Ethynyl]Imidazo[1,2-B]Pyridazine within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn802

b:48.4
occ:1.00
 O D:HOH932 2.0 37.9 1.0
O D:HOH930 2.2 43.4 1.0
NE2 D:HIS563 2.2 38.1 1.0
NE2 D:HIS529 2.2 44.2 1.0
OD2 D:ASP564 2.2 52.9 1.0
OD1 D:ASP674 2.4 44.4 1.0
CD2 D:HIS563 3.0 39.6 1.0
CD2 D:HIS529 3.1 52.0 1.0
CG D:ASP674 3.2 44.1 1.0
CG D:ASP564 3.2 40.8 1.0
CE1 D:HIS529 3.3 49.5 1.0
CE1 D:HIS563 3.4 39.9 1.0
OD2 D:ASP674 3.4 49.1 1.0
OD1 D:ASP564 3.7 42.4 1.0
MG D:MG803 3.8 48.4 1.0
O D:HOH920 4.0 41.3 1.0
O D:HOH904 4.1 45.5 1.0
CD2 D:HIS525 4.2 45.5 1.0
CG D:HIS563 4.2 39.1 1.0
CB D:ASP564 4.3 40.3 1.0
CG D:HIS529 4.3 45.7 1.0
ND1 D:HIS529 4.3 47.5 1.0
ND1 D:HIS563 4.4 38.8 1.0
NE2 D:HIS525 4.5 55.8 1.0
CB D:ASP674 4.5 42.9 1.0
O D:HOH913 4.6 41.6 1.0
CG2 D:VAL533 4.7 49.7 1.0
O D:ASP674 4.8 46.3 1.0
CA D:ASP674 4.9 46.5 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 04:50:43 2024

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