Atomistry » Zinc » PDB 5aml-5b3h » 5axp
Atomistry »
  Zinc »
    PDB 5aml-5b3h »
      5axp »

Zinc in PDB 5axp: Crystal Structure of the Catalytic Domain of PDE10A Complexed with 1- (2-Fluoro-4-(2-Oxo-1,3-Oxazolidin-3-Yl)Phenyl)-5-Methoxy-3-(1-Phenyl- 1H-Pyrazol-5-Yl)Pyridazin-4(1H)-One

Enzymatic activity of Crystal Structure of the Catalytic Domain of PDE10A Complexed with 1- (2-Fluoro-4-(2-Oxo-1,3-Oxazolidin-3-Yl)Phenyl)-5-Methoxy-3-(1-Phenyl- 1H-Pyrazol-5-Yl)Pyridazin-4(1H)-One

All present enzymatic activity of Crystal Structure of the Catalytic Domain of PDE10A Complexed with 1- (2-Fluoro-4-(2-Oxo-1,3-Oxazolidin-3-Yl)Phenyl)-5-Methoxy-3-(1-Phenyl- 1H-Pyrazol-5-Yl)Pyridazin-4(1H)-One:
3.1.4.17; 3.1.4.35;

Protein crystallography data

The structure of Crystal Structure of the Catalytic Domain of PDE10A Complexed with 1- (2-Fluoro-4-(2-Oxo-1,3-Oxazolidin-3-Yl)Phenyl)-5-Methoxy-3-(1-Phenyl- 1H-Pyrazol-5-Yl)Pyridazin-4(1H)-One, PDB code: 5axp 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 / 1.95
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 49.753, 81.849, 159.684, 90.00, 90.00, 90.00
R / Rfree (%) 17.6 / 23.4

Other elements in 5axp:

The structure of Crystal Structure of the Catalytic Domain of PDE10A Complexed with 1- (2-Fluoro-4-(2-Oxo-1,3-Oxazolidin-3-Yl)Phenyl)-5-Methoxy-3-(1-Phenyl- 1H-Pyrazol-5-Yl)Pyridazin-4(1H)-One 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 1- (2-Fluoro-4-(2-Oxo-1,3-Oxazolidin-3-Yl)Phenyl)-5-Methoxy-3-(1-Phenyl- 1H-Pyrazol-5-Yl)Pyridazin-4(1H)-One (pdb code 5axp). 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 1- (2-Fluoro-4-(2-Oxo-1,3-Oxazolidin-3-Yl)Phenyl)-5-Methoxy-3-(1-Phenyl- 1H-Pyrazol-5-Yl)Pyridazin-4(1H)-One, PDB code: 5axp:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in 5axp

Go back to Zinc Binding Sites List in 5axp
Zinc binding site 1 out of 2 in the Crystal Structure of the Catalytic Domain of PDE10A Complexed with 1- (2-Fluoro-4-(2-Oxo-1,3-Oxazolidin-3-Yl)Phenyl)-5-Methoxy-3-(1-Phenyl- 1H-Pyrazol-5-Yl)Pyridazin-4(1H)-One


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 1- (2-Fluoro-4-(2-Oxo-1,3-Oxazolidin-3-Yl)Phenyl)-5-Methoxy-3-(1-Phenyl- 1H-Pyrazol-5-Yl)Pyridazin-4(1H)-One within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1002

b:32.8
occ:1.00
 OD2 A:ASP554 2.1 24.8 1.0
NE2 A:HIS553 2.2 26.8 1.0
OD1 A:ASP664 2.2 25.4 1.0
NE2 A:HIS519 2.2 24.6 1.0
O A:HOH1108 2.3 23.8 1.0
O A:HOH1155 2.4 27.1 1.0
CD2 A:HIS553 3.0 23.4 1.0
CG A:ASP664 3.1 29.1 1.0
CG A:ASP554 3.2 26.0 1.0
CD2 A:HIS519 3.2 24.5 1.0
CE1 A:HIS553 3.2 24.6 1.0
CE1 A:HIS519 3.2 22.8 1.0
OD2 A:ASP664 3.3 35.6 1.0
OD1 A:ASP554 3.6 24.3 1.0
MG A:MG1001 3.8 28.5 1.0
CD2 A:HIS515 4.0 29.2 1.0
O A:HOH1178 4.1 27.2 1.0
O A:HOH1141 4.1 25.3 1.0
CG A:HIS553 4.2 26.6 1.0
ND1 A:HIS553 4.3 24.2 1.0
ND1 A:HIS519 4.3 26.3 1.0
CG A:HIS519 4.3 24.0 1.0
NE2 A:HIS515 4.4 30.7 1.0
CB A:ASP554 4.4 25.2 1.0
CB A:ASP664 4.5 21.7 1.0
O A:HOH1228 4.6 53.1 1.0
CG2 A:VAL523 4.8 18.9 1.0
O A:HOH1104 4.8 26.9 1.0
CA A:ASP664 4.8 23.6 1.0
O A:ASP664 4.9 25.2 1.0

Zinc binding site 2 out of 2 in 5axp

Go back to Zinc Binding Sites List in 5axp
Zinc binding site 2 out of 2 in the Crystal Structure of the Catalytic Domain of PDE10A Complexed with 1- (2-Fluoro-4-(2-Oxo-1,3-Oxazolidin-3-Yl)Phenyl)-5-Methoxy-3-(1-Phenyl- 1H-Pyrazol-5-Yl)Pyridazin-4(1H)-One


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 1- (2-Fluoro-4-(2-Oxo-1,3-Oxazolidin-3-Yl)Phenyl)-5-Methoxy-3-(1-Phenyl- 1H-Pyrazol-5-Yl)Pyridazin-4(1H)-One within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn1002

b:31.0
occ:1.00
 OD2 B:ASP554 2.1 27.0 1.0
NE2 B:HIS553 2.1 23.4 1.0
OD1 B:ASP664 2.2 24.7 1.0
O B:HOH1124 2.2 22.1 1.0
NE2 B:HIS519 2.2 25.3 1.0
O B:HOH1138 2.4 30.3 1.0
CD2 B:HIS553 3.0 24.0 1.0
CG B:ASP664 3.1 32.0 1.0
CD2 B:HIS519 3.1 25.6 1.0
CG B:ASP554 3.1 27.5 1.0
CE1 B:HIS553 3.2 22.0 1.0
CE1 B:HIS519 3.2 25.7 1.0
OD2 B:ASP664 3.3 39.0 1.0
OD1 B:ASP554 3.6 25.1 1.0
MG B:MG1001 3.8 28.3 1.0
O B:HOH1171 4.0 28.1 1.0
CD2 B:HIS515 4.1 30.4 1.0
O B:HOH1132 4.2 25.3 1.0
CG B:HIS553 4.2 25.1 1.0
ND1 B:HIS553 4.2 22.8 1.0
CG B:HIS519 4.3 25.5 1.0
ND1 B:HIS519 4.3 22.7 1.0
NE2 B:HIS515 4.3 30.4 1.0
CB B:ASP554 4.4 24.7 1.0
CB B:ASP664 4.4 30.3 1.0
O B:HOH1109 4.7 27.2 1.0
CG2 B:VAL523 4.8 22.6 1.0
CA B:ASP664 4.8 24.6 1.0
O B:ASP664 4.9 25.4 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: Sun Oct 27 13:14:14 2024

Last articles

Zn in 9J0N
Zn in 9J0O
Zn in 9J0P
Zn in 9FJX
Zn in 9EKB
Zn in 9C0F
Zn in 9CAH
Zn in 9CH0
Zn in 9CH3
Zn in 9CH1
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy