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Zinc in PDB 5b4k: Crystal Structure of the Catalytic Domain of Human PDE10A Complexed with N-(4-((5-Methyl-5H-Pyrrolo[3,2-D]Pyrimidin-4-Yl)Oxy)Phenyl)-1H- Benzimidazol-2-Amine

Enzymatic activity of Crystal Structure of the Catalytic Domain of Human PDE10A Complexed with N-(4-((5-Methyl-5H-Pyrrolo[3,2-D]Pyrimidin-4-Yl)Oxy)Phenyl)-1H- Benzimidazol-2-Amine

All present enzymatic activity of Crystal Structure of the Catalytic Domain of Human PDE10A Complexed with N-(4-((5-Methyl-5H-Pyrrolo[3,2-D]Pyrimidin-4-Yl)Oxy)Phenyl)-1H- Benzimidazol-2-Amine:
3.1.4.17;

Protein crystallography data

The structure of Crystal Structure of the Catalytic Domain of Human PDE10A Complexed with N-(4-((5-Methyl-5H-Pyrrolo[3,2-D]Pyrimidin-4-Yl)Oxy)Phenyl)-1H- Benzimidazol-2-Amine, PDB code: 5b4k was solved by H.Oki, Y.Zama, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 80.83 / 2.90
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 49.734, 81.683, 161.654, 90.00, 90.00, 90.00
R / Rfree (%) 17.7 / 26.1

Other elements in 5b4k:

The structure of Crystal Structure of the Catalytic Domain of Human PDE10A Complexed with N-(4-((5-Methyl-5H-Pyrrolo[3,2-D]Pyrimidin-4-Yl)Oxy)Phenyl)-1H- Benzimidazol-2-Amine also contains other interesting chemical elements:

Magnesium (Mg) 2 atoms

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of the Catalytic Domain of Human PDE10A Complexed with N-(4-((5-Methyl-5H-Pyrrolo[3,2-D]Pyrimidin-4-Yl)Oxy)Phenyl)-1H- Benzimidazol-2-Amine (pdb code 5b4k). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 2 binding sites of Zinc where determined in the Crystal Structure of the Catalytic Domain of Human PDE10A Complexed with N-(4-((5-Methyl-5H-Pyrrolo[3,2-D]Pyrimidin-4-Yl)Oxy)Phenyl)-1H- Benzimidazol-2-Amine, PDB code: 5b4k:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in 5b4k

Go back to Zinc Binding Sites List in 5b4k
Zinc binding site 1 out of 2 in the Crystal Structure of the Catalytic Domain of Human PDE10A Complexed with N-(4-((5-Methyl-5H-Pyrrolo[3,2-D]Pyrimidin-4-Yl)Oxy)Phenyl)-1H- Benzimidazol-2-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 the Catalytic Domain of Human PDE10A Complexed with N-(4-((5-Methyl-5H-Pyrrolo[3,2-D]Pyrimidin-4-Yl)Oxy)Phenyl)-1H- Benzimidazol-2-Amine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1002

b:64.5
occ:1.00
 OD2 A:ASP554 2.1 40.9 1.0
OD1 A:ASP664 2.1 45.6 1.0
NE2 A:HIS519 2.2 38.3 1.0
NE2 A:HIS553 2.3 43.7 1.0
O A:HOH1137 2.3 43.5 1.0
O A:HOH1117 2.6 60.2 1.0
CE1 A:HIS519 3.1 36.7 1.0
CD2 A:HIS553 3.1 43.3 1.0
CG A:ASP664 3.1 47.2 1.0
CG A:ASP554 3.2 38.9 1.0
CD2 A:HIS519 3.2 38.3 1.0
CE1 A:HIS553 3.3 44.1 1.0
OD2 A:ASP664 3.4 50.8 1.0
OD1 A:ASP554 3.7 38.1 1.0
MG A:MG1001 3.9 30.1 1.0
O A:HOH1104 3.9 35.2 1.0
CD2 A:HIS515 4.0 48.4 1.0
O A:HOH1127 4.0 41.8 1.0
ND1 A:HIS519 4.2 35.0 1.0
CG A:HIS553 4.3 42.9 1.0
CG A:HIS519 4.3 37.5 1.0
ND1 A:HIS553 4.3 43.7 1.0
CB A:ASP554 4.4 36.9 1.0
NE2 A:HIS515 4.4 46.3 1.0
CB A:ASP664 4.5 44.6 1.0
CG2 A:VAL523 4.8 37.1 1.0
CA A:ASP664 4.9 42.1 1.0
O A:ASP664 4.9 52.9 1.0
O A:HOH1112 4.9 24.1 1.0

Zinc binding site 2 out of 2 in 5b4k

Go back to Zinc Binding Sites List in 5b4k
Zinc binding site 2 out of 2 in the Crystal Structure of the Catalytic Domain of Human PDE10A Complexed with N-(4-((5-Methyl-5H-Pyrrolo[3,2-D]Pyrimidin-4-Yl)Oxy)Phenyl)-1H- Benzimidazol-2-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 the Catalytic Domain of Human PDE10A Complexed with N-(4-((5-Methyl-5H-Pyrrolo[3,2-D]Pyrimidin-4-Yl)Oxy)Phenyl)-1H- Benzimidazol-2-Amine within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn1002

b:59.1
occ:1.00
 NE2 B:HIS553 2.1 38.5 1.0
OD2 B:ASP554 2.1 40.2 1.0
O B:HOH1136 2.2 30.7 1.0
OD1 B:ASP664 2.2 45.4 1.0
NE2 B:HIS519 2.2 41.0 1.0
CD2 B:HIS553 2.9 40.2 1.0
CG B:ASP664 3.1 44.9 1.0
CE1 B:HIS519 3.1 41.6 1.0
CG B:ASP554 3.2 37.5 1.0
CE1 B:HIS553 3.2 41.0 1.0
CD2 B:HIS519 3.3 40.1 1.0
OD2 B:ASP664 3.3 43.8 1.0
OD1 B:ASP554 3.6 37.4 1.0
MG B:MG1001 3.8 55.2 1.0
O B:HOH1107 3.8 36.2 1.0
O B:HOH1141 3.9 42.4 1.0
CD2 B:HIS515 4.0 61.5 1.0
CG B:HIS553 4.1 39.8 1.0
ND1 B:HIS553 4.2 39.1 1.0
ND1 B:HIS519 4.3 41.0 1.0
CB B:ASP554 4.3 37.4 1.0
CG B:HIS519 4.4 40.3 1.0
NE2 B:HIS515 4.4 63.5 1.0
CB B:ASP664 4.5 43.5 1.0
O B:HOH1102 4.7 42.7 1.0
CG2 B:VAL523 4.8 28.6 1.0
O B:ASP664 4.9 46.5 1.0
CA B:ASP664 4.9 43.0 1.0

Reference:

M.Yoshikawa, T.Hitaka, T.Hasui, M.Fushimi, J.Kunitomo, H.Kokubo, H.Oki, K.Nakashima, T.Taniguchi. Design and Synthesis of Potent and Selective Pyridazin-4(1H)-One-Based PDE10A Inhibitors Interacting with TYR683 in the PDE10A Selectivity Pocket Bioorg.Med.Chem. V. 24 3447 2016.
ISSN: ESSN 1464-3391
PubMed: 27301679
DOI: 10.1016/J.BMC.2016.05.049
Page generated: Sun Oct 27 13:20:31 2024

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