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Zinc in PDB 5axq: Crystal Structure of the Catalytic Domain of PDE10A Complexed with Highly Potent and Brain-Penetrant PDE10A Inhibitor with 2-Oxindole Scaffold

Enzymatic activity of Crystal Structure of the Catalytic Domain of PDE10A Complexed with Highly Potent and Brain-Penetrant PDE10A Inhibitor with 2-Oxindole Scaffold

All present enzymatic activity of Crystal Structure of the Catalytic Domain of PDE10A Complexed with Highly Potent and Brain-Penetrant PDE10A Inhibitor with 2-Oxindole Scaffold:
3.1.4.17; 3.1.4.35;

Protein crystallography data

The structure of Crystal Structure of the Catalytic Domain of PDE10A Complexed with Highly Potent and Brain-Penetrant PDE10A Inhibitor with 2-Oxindole Scaffold, PDB code: 5axq 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) 50.00 / 1.77
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 49.685, 81.793, 159.849, 90.00, 90.00, 90.00
R / Rfree (%) 17.1 / 21.1

Other elements in 5axq:

The structure of Crystal Structure of the Catalytic Domain of PDE10A Complexed with Highly Potent and Brain-Penetrant PDE10A Inhibitor with 2-Oxindole Scaffold also contains other interesting chemical elements:

Fluorine (F) 2 atoms
Magnesium (Mg) 2 atoms

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of the Catalytic Domain of PDE10A Complexed with Highly Potent and Brain-Penetrant PDE10A Inhibitor with 2-Oxindole Scaffold (pdb code 5axq). 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 PDE10A Complexed with Highly Potent and Brain-Penetrant PDE10A Inhibitor with 2-Oxindole Scaffold, PDB code: 5axq:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in 5axq

Go back to Zinc Binding Sites List in 5axq
Zinc binding site 1 out of 2 in the Crystal Structure of the Catalytic Domain of PDE10A Complexed with Highly Potent and Brain-Penetrant PDE10A Inhibitor with 2-Oxindole Scaffold


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 PDE10A Complexed with Highly Potent and Brain-Penetrant PDE10A Inhibitor with 2-Oxindole Scaffold within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1002

b:30.2
occ:1.00
OD2 A:ASP554 2.1 20.5 1.0
O A:HOH1118 2.1 20.4 1.0
OD1 A:ASP664 2.1 20.6 1.0
NE2 A:HIS519 2.2 23.3 1.0
NE2 A:HIS553 2.3 23.3 1.0
O A:HOH1201 2.4 25.4 1.0
CG A:ASP664 3.1 26.8 1.0
CG A:ASP554 3.1 21.7 1.0
CD2 A:HIS553 3.1 20.1 1.0
CD2 A:HIS519 3.2 22.1 1.0
CE1 A:HIS519 3.3 20.7 1.0
CE1 A:HIS553 3.3 20.5 1.0
OD2 A:ASP664 3.3 30.9 1.0
OD1 A:ASP554 3.6 23.7 1.0
MG A:MG1001 3.8 25.0 1.0
O A:HOH1258 4.0 23.5 1.0
CD2 A:HIS515 4.1 26.9 1.0
O A:HOH1123 4.2 25.0 1.0
CG A:HIS553 4.3 21.5 1.0
CG A:HIS519 4.3 23.8 1.0
ND1 A:HIS519 4.4 23.1 1.0
ND1 A:HIS553 4.4 22.6 1.0
CB A:ASP554 4.4 21.8 1.0
NE2 A:HIS515 4.4 26.2 1.0
CB A:ASP664 4.4 20.6 1.0
O A:HOH1239 4.4 36.2 1.0
O A:HOH1122 4.7 24.4 1.0
CA A:ASP664 4.8 21.5 1.0
CG2 A:VAL523 4.8 20.0 1.0
O A:ASP664 4.9 21.1 1.0

Zinc binding site 2 out of 2 in 5axq

Go back to Zinc Binding Sites List in 5axq
Zinc binding site 2 out of 2 in the Crystal Structure of the Catalytic Domain of PDE10A Complexed with Highly Potent and Brain-Penetrant PDE10A Inhibitor with 2-Oxindole Scaffold


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 PDE10A Complexed with Highly Potent and Brain-Penetrant PDE10A Inhibitor with 2-Oxindole Scaffold within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn1002

b:27.0
occ:1.00
OD2 B:ASP554 2.1 22.4 1.0
O B:HOH1117 2.1 20.6 1.0
OD1 B:ASP664 2.2 21.6 1.0
NE2 B:HIS553 2.2 18.8 1.0
NE2 B:HIS519 2.2 21.4 1.0
O B:HOH1152 2.3 24.8 1.0
CD2 B:HIS553 3.1 21.7 1.0
CG B:ASP664 3.1 28.6 1.0
CG B:ASP554 3.1 24.0 1.0
CD2 B:HIS519 3.1 21.3 1.0
CE1 B:HIS519 3.2 20.8 1.0
CE1 B:HIS553 3.2 18.8 1.0
OD2 B:ASP664 3.3 33.7 1.0
OD1 B:ASP554 3.5 23.5 1.0
MG B:MG1001 3.7 23.1 1.0
CD2 B:HIS515 4.0 23.9 1.0
O B:HOH1226 4.1 22.1 1.0
O B:HOH1133 4.2 22.7 1.0
CG B:HIS553 4.2 21.5 1.0
ND1 B:HIS553 4.3 20.6 1.0
CG B:HIS519 4.3 20.9 1.0
NE2 B:HIS515 4.3 26.2 1.0
ND1 B:HIS519 4.3 20.8 1.0
CB B:ASP554 4.3 23.6 1.0
CB B:ASP664 4.4 23.6 1.0
O B:HOH1207 4.5 43.9 1.0
O B:HOH1112 4.6 22.6 1.0
CG2 B:VAL523 4.8 18.7 1.0
CA B:ASP664 4.8 21.2 1.0
O B:ASP664 4.9 20.8 1.0

Reference:

M.Yoshikawa, H.Kamisaki, J.Kunitomo, H.Oki, H.Kokubo, A.Suzuki, T.Ikemoto, K.Nakashima, N.Kamiguchi, A.Harada, H.Kimura, T.Taniguchi. Design and Synthesis of A Novel 2-Oxindole Scaffold As A Highly Potent and Brain-Penetrant Phosphodiesterase 10A Inhibitor Bioorg.Med.Chem. V. 23 7138 2015.
ISSN: ESSN 1464-3391
PubMed: 26494583
DOI: 10.1016/J.BMC.2015.10.002
Page generated: Wed Dec 16 06:04:06 2020

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