Atomistry » Zinc » PDB 5seq-5sft » 5sf1
Atomistry »
  Zinc »
    PDB 5seq-5sft »
      5sf1 »

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

Last articles

Zn in 9JYW
Zn in 9IR4
Zn in 9IR3
Zn in 9GMX
Zn in 9GMW
Zn in 9JEJ
Zn in 9ERF
Zn in 9ERE
Zn in 9EGV
Zn in 9EGW
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy