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Nickel in PDB 4mse: Crystal Structure of PDE10A2 with Fragment ZT1597 (2-({[(2S)-2-Methyl- 2,3-Dihydro-1,3-Benzothiazol-5-Yl]Oxy}Methyl)Quinoline)

Enzymatic activity of Crystal Structure of PDE10A2 with Fragment ZT1597 (2-({[(2S)-2-Methyl- 2,3-Dihydro-1,3-Benzothiazol-5-Yl]Oxy}Methyl)Quinoline)

All present enzymatic activity of Crystal Structure of PDE10A2 with Fragment ZT1597 (2-({[(2S)-2-Methyl- 2,3-Dihydro-1,3-Benzothiazol-5-Yl]Oxy}Methyl)Quinoline):
3.1.4.17; 3.1.4.35;

Protein crystallography data

The structure of Crystal Structure of PDE10A2 with Fragment ZT1597 (2-({[(2S)-2-Methyl- 2,3-Dihydro-1,3-Benzothiazol-5-Yl]Oxy}Methyl)Quinoline), PDB code: 4mse was solved by V.Sridhar, J.Badger, C.Logan, B.Chie-Leon, V.Nienaber, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 48.20 / 2.81
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 50.652, 81.819, 156.850, 90.00, 90.00, 90.00
R / Rfree (%) 27.1 / 34.3

Nickel Binding Sites:

The binding sites of Nickel atom in the Crystal Structure of PDE10A2 with Fragment ZT1597 (2-({[(2S)-2-Methyl- 2,3-Dihydro-1,3-Benzothiazol-5-Yl]Oxy}Methyl)Quinoline) (pdb code 4mse). This binding sites where shown within 5.0 Angstroms radius around Nickel atom.
In total 4 binding sites of Nickel where determined in the Crystal Structure of PDE10A2 with Fragment ZT1597 (2-({[(2S)-2-Methyl- 2,3-Dihydro-1,3-Benzothiazol-5-Yl]Oxy}Methyl)Quinoline), PDB code: 4mse:
Jump to Nickel binding site number: 1; 2; 3; 4;

Nickel binding site 1 out of 4 in 4mse

Go back to Nickel Binding Sites List in 4mse
Nickel binding site 1 out of 4 in the Crystal Structure of PDE10A2 with Fragment ZT1597 (2-({[(2S)-2-Methyl- 2,3-Dihydro-1,3-Benzothiazol-5-Yl]Oxy}Methyl)Quinoline)


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 1 of Crystal Structure of PDE10A2 with Fragment ZT1597 (2-({[(2S)-2-Methyl- 2,3-Dihydro-1,3-Benzothiazol-5-Yl]Oxy}Methyl)Quinoline) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ni901

b:72.0
occ:1.00
 NE2 A:HIS563 2.0 73.1 1.0
OD2 A:ASP564 2.1 75.1 1.0
OD2 A:ASP674 2.2 65.3 1.0
NE2 A:HIS529 2.3 59.5 1.0
CD2 A:HIS563 2.8 73.9 1.0
CG A:ASP674 2.9 64.6 1.0
CG A:ASP564 3.0 74.5 1.0
OD1 A:ASP674 3.1 64.4 1.0
CD2 A:HIS529 3.1 61.2 1.0
CE1 A:HIS563 3.1 73.4 1.0
CE1 A:HIS529 3.4 60.8 1.0
OD1 A:ASP564 3.6 72.7 1.0
NI A:NI902 3.6 0.1 1.0
CG A:HIS563 4.0 74.1 1.0
CD2 A:HIS525 4.1 61.9 1.0
ND1 A:HIS563 4.1 73.5 1.0
CB A:ASP564 4.2 75.4 1.0
CG A:HIS529 4.3 61.8 1.0
CB A:ASP674 4.3 65.1 1.0
ND1 A:HIS529 4.4 61.2 1.0
NE2 A:HIS525 4.5 62.6 1.0
O A:ASP674 4.7 64.8 1.0
CA A:ASP674 4.9 64.9 1.0
CG2 A:VAL533 5.0 64.6 1.0

Nickel binding site 2 out of 4 in 4mse

Go back to Nickel Binding Sites List in 4mse
Nickel binding site 2 out of 4 in the Crystal Structure of PDE10A2 with Fragment ZT1597 (2-({[(2S)-2-Methyl- 2,3-Dihydro-1,3-Benzothiazol-5-Yl]Oxy}Methyl)Quinoline)


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 2 of Crystal Structure of PDE10A2 with Fragment ZT1597 (2-({[(2S)-2-Methyl- 2,3-Dihydro-1,3-Benzothiazol-5-Yl]Oxy}Methyl)Quinoline) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ni902

b:0.1
occ:1.00
 OD1 A:ASP564 2.3 72.7 1.0
CG A:ASP564 3.2 74.5 1.0
OD2 A:ASP564 3.3 75.1 1.0
NI A:NI901 3.6 72.0 1.0
OE2 A:GLU592 4.2 80.7 1.0
CD2 A:HIS525 4.2 61.9 1.0
CD2 A:HIS563 4.3 73.9 1.0
OD1 A:ASP674 4.3 64.4 1.0
NE2 A:HIS525 4.3 62.6 1.0
NE2 A:HIS595 4.5 83.8 1.0
O A:THR633 4.6 59.9 1.0
NE2 A:HIS563 4.6 73.1 1.0
CB A:ASP564 4.6 75.4 1.0
O A:HIS563 4.6 75.0 1.0
CD2 A:HIS595 4.7 84.6 1.0
CD2 A:HIS567 4.8 78.5 1.0
OG1 A:THR633 4.8 59.3 1.0
CB A:THR633 4.9 59.7 1.0
NE2 A:HIS567 5.0 78.8 1.0

Nickel binding site 3 out of 4 in 4mse

Go back to Nickel Binding Sites List in 4mse
Nickel binding site 3 out of 4 in the Crystal Structure of PDE10A2 with Fragment ZT1597 (2-({[(2S)-2-Methyl- 2,3-Dihydro-1,3-Benzothiazol-5-Yl]Oxy}Methyl)Quinoline)


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 3 of Crystal Structure of PDE10A2 with Fragment ZT1597 (2-({[(2S)-2-Methyl- 2,3-Dihydro-1,3-Benzothiazol-5-Yl]Oxy}Methyl)Quinoline) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ni901

b:73.7
occ:1.00
 OD1 B:ASP674 2.1 64.0 1.0
NE2 B:HIS529 2.2 66.8 1.0
OD2 B:ASP564 2.2 82.3 1.0
NE2 B:HIS563 2.3 77.9 1.0
CG B:ASP674 3.0 64.0 1.0
CD2 B:HIS563 3.1 78.6 1.0
CE1 B:HIS529 3.2 67.8 1.0
CD2 B:HIS529 3.2 68.5 1.0
CG B:ASP564 3.2 83.3 1.0
OD2 B:ASP674 3.2 65.4 1.0
CE1 B:HIS563 3.4 77.6 1.0
NI B:NI902 3.5 0.1 1.0
OD1 B:ASP564 3.6 82.2 1.0
CG B:HIS563 4.3 79.5 1.0
ND1 B:HIS529 4.3 68.7 1.0
CG B:HIS529 4.3 69.8 1.0
ND1 B:HIS563 4.4 77.8 1.0
CB B:ASP674 4.5 62.8 1.0
CB B:ASP564 4.5 84.0 1.0
CD2 B:HIS525 4.6 91.0 1.0
CA B:ASP674 4.9 62.6 1.0
CG2 B:VAL533 4.9 67.8 1.0

Nickel binding site 4 out of 4 in 4mse

Go back to Nickel Binding Sites List in 4mse
Nickel binding site 4 out of 4 in the Crystal Structure of PDE10A2 with Fragment ZT1597 (2-({[(2S)-2-Methyl- 2,3-Dihydro-1,3-Benzothiazol-5-Yl]Oxy}Methyl)Quinoline)


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 4 of Crystal Structure of PDE10A2 with Fragment ZT1597 (2-({[(2S)-2-Methyl- 2,3-Dihydro-1,3-Benzothiazol-5-Yl]Oxy}Methyl)Quinoline) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ni902

b:0.1
occ:1.00
 OD1 B:ASP564 2.0 82.2 1.0
CG B:ASP564 3.0 83.3 1.0
OD2 B:ASP564 3.3 82.3 1.0
NI B:NI901 3.5 73.7 1.0
OE2 B:GLU592 3.8 0.5 1.0
NE2 B:HIS595 4.0 1.0 1.0
CD2 B:HIS567 4.1 96.8 1.0
NE2 B:HIS567 4.1 97.1 1.0
CD2 B:HIS563 4.2 78.6 1.0
O B:HIS563 4.3 82.4 1.0
CD2 B:HIS595 4.3 0.4 1.0
CB B:ASP564 4.4 84.0 1.0
CD2 B:HIS525 4.4 91.0 1.0
OG1 B:THR633 4.5 80.5 1.0
NE2 B:HIS563 4.5 77.9 1.0
O B:THR633 4.6 80.0 1.0
CA B:ASP564 4.6 84.6 1.0
CD B:GLU592 4.9 0.5 1.0
CB B:THR633 4.9 80.0 1.0
CE1 B:HIS595 4.9 0.1 1.0
C B:HIS563 5.0 82.6 1.0
OD2 B:ASP674 5.0 65.4 1.0

Reference:

M.I.Recht, V.Sridhar, J.Badger, P.Y.Bounaud, C.Logan, B.Chie-Leon, V.Nienaber, F.E.Torres. Identification and Optimization of PDE10A Inhibitors Using Fragment-Based Screening By Nanocalorimetry and X-Ray Crystallography. J Biomol Screen V. 19 497 2014.
ISSN: ISSN 1087-0571
PubMed: 24375910
DOI: 10.1177/1087057113516493
Page generated: Wed Oct 9 18:30:40 2024

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