Nickel in PDB 4msc: Crystal Structure of PDE10A2 with Fragment ZT1595 (2-[(Quinolin-7- Yloxy)Methyl]Quinoline)

All present enzymatic activity of Crystal Structure of PDE10A2 with Fragment ZT1595 (2-[(Quinolin-7- Yloxy)Methyl]Quinoline):
3.1.4.17; 3.1.4.35;

The structure of Crystal Structure of PDE10A2 with Fragment ZT1595 (2-[(Quinolin-7- Yloxy)Methyl]Quinoline), PDB code: 4msc 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)	48.80 / 2.47
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	51.380, 82.085, 155.926, 90.00, 90.00, 90.00
R / Rfree (%)	23.4 / 28.1

The binding sites of Nickel atom in the Crystal Structure of PDE10A2 with Fragment ZT1595 (2-[(Quinolin-7- Yloxy)Methyl]Quinoline) (pdb code 4msc). 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 ZT1595 (2-[(Quinolin-7- Yloxy)Methyl]Quinoline), PDB code: 4msc:
Jump to Nickel binding site number: 1; 2; 3; 4;

Nickel binding site 1 out of 4 in the Crystal Structure of PDE10A2 with Fragment ZT1595 (2-[(Quinolin-7- Yloxy)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 ZT1595 (2-[(Quinolin-7- Yloxy)Methyl]Quinoline) within 5.0Å range: probe atom residue distance (Å) B Occ A:Ni901 b:48.9 occ:1.00 O A:HOH1019 1.8 36.0 1.0 NE2 A:HIS563 2.1 46.9 1.0 NE2 A:HIS529 2.1 43.3 1.0 OD2 A:ASP564 2.2 44.2 1.0 OD2 A:ASP674 2.2 40.8 1.0 CE1 A:HIS563 3.0 48.6 1.0 CE1 A:HIS529 3.0 43.7 1.0 CD2 A:HIS563 3.1 47.0 1.0 CD2 A:HIS529 3.1 44.9 1.0 CG A:ASP564 3.1 45.6 1.0 CG A:ASP674 3.1 42.1 1.0 O A:HOH1001 3.2 39.2 1.0 OD1 A:ASP674 3.4 41.7 1.0 OD1 A:ASP564 3.6 44.1 1.0 NI A:NI902 3.7 67.4 1.0 ND1 A:HIS563 4.1 47.0 1.0 CD2 A:HIS525 4.1 47.8 1.0 ND1 A:HIS529 4.1 44.6 1.0 CG A:HIS563 4.2 46.5 1.0 CG A:HIS529 4.2 45.6 1.0 O A:HOH1018 4.2 46.4 1.0 CB A:ASP564 4.3 47.0 1.0 CB A:ASP674 4.5 42.5 1.0 O A:HOH1021 4.6 49.4 1.0 NE2 A:HIS525 4.7 47.6 1.0 CA A:ASP674 4.9 42.5 1.0 O A:ASP674 4.9 44.7 1.0

Nickel binding site 2 out of 4 in the Crystal Structure of PDE10A2 with Fragment ZT1595 (2-[(Quinolin-7- Yloxy)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 ZT1595 (2-[(Quinolin-7- Yloxy)Methyl]Quinoline) within 5.0Å range: probe atom residue distance (Å) B Occ A:Ni902 b:67.4 occ:1.00 O A:HOH1018 1.9 46.4 1.0 OD1 A:ASP564 2.2 44.1 1.0 O A:HOH1020 2.2 37.3 1.0 O A:HOH1019 2.2 36.0 1.0 O A:HOH1022 2.3 37.2 1.0 O A:HOH1021 2.3 49.4 1.0 CG A:ASP564 3.2 45.6 1.0 OD2 A:ASP564 3.5 44.2 1.0 NI A:NI901 3.7 48.9 1.0 OE2 A:GLU592 4.1 42.8 1.0 CD2 A:HIS563 4.2 47.0 1.0 OG1 A:THR633 4.2 41.1 1.0 NE2 A:HIS595 4.2 55.1 1.0 O A:HIS563 4.3 45.0 1.0 O A:THR633 4.3 43.1 1.0 NE2 A:HIS563 4.4 46.9 1.0 CD2 A:HIS595 4.4 56.2 1.0 OD1 A:ASP674 4.5 41.7 1.0 CB A:ASP564 4.6 47.0 1.0 CD2 A:HIS567 4.6 50.3 1.0 CB A:THR633 4.6 41.7 1.0 O A:HOH1001 4.8 39.2 1.0 NE2 A:HIS567 4.8 50.3 1.0 CD2 A:HIS525 4.8 47.8 1.0 CA A:ASP564 4.9 47.4 1.0 CD A:GLU592 4.9 45.1 1.0 CG A:GLU592 4.9 47.6 1.0

Nickel binding site 3 out of 4 in the Crystal Structure of PDE10A2 with Fragment ZT1595 (2-[(Quinolin-7- Yloxy)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 ZT1595 (2-[(Quinolin-7- Yloxy)Methyl]Quinoline) within 5.0Å range: probe atom residue distance (Å) B Occ B:Ni901 b:50.8 occ:1.00 O B:HOH1011 2.0 52.0 1.0 OD2 B:ASP564 2.1 48.2 1.0 OD1 B:ASP674 2.1 37.7 1.0 NE2 B:HIS563 2.2 44.8 1.0 O B:HOH1006 2.2 48.5 1.0 NE2 B:HIS529 2.2 45.5 1.0 CD2 B:HIS563 3.0 44.2 1.0 CG B:ASP674 3.0 39.4 1.0 CG B:ASP564 3.1 47.6 1.0 CD2 B:HIS529 3.2 47.8 1.0 OD2 B:ASP674 3.2 42.7 1.0 CE1 B:HIS529 3.2 45.9 1.0 CE1 B:HIS563 3.3 44.4 1.0 OD1 B:ASP564 3.6 43.4 1.0 NI B:NI902 4.0 77.7 1.0 O B:HOH1007 4.2 43.2 1.0 CG B:HIS563 4.2 45.2 1.0 CB B:ASP564 4.3 48.4 1.0 ND1 B:HIS563 4.3 44.2 1.0 ND1 B:HIS529 4.3 46.2 1.0 CG B:HIS529 4.3 46.9 1.0 CD2 B:HIS525 4.4 68.4 1.0 CB B:ASP674 4.4 40.1 1.0 O B:HOH1009 4.5 41.9 1.0 CG2 B:VAL533 4.8 42.8 1.0 CA B:ASP674 4.9 40.8 1.0 O B:HOH1010 4.9 51.0 1.0

Nickel binding site 4 out of 4 in the Crystal Structure of PDE10A2 with Fragment ZT1595 (2-[(Quinolin-7- Yloxy)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 ZT1595 (2-[(Quinolin-7- Yloxy)Methyl]Quinoline) within 5.0Å range: probe atom residue distance (Å) B Occ B:Ni902 b:77.7 occ:1.00 O B:HOH1010 2.2 51.0 1.0 OD1 B:ASP564 2.2 43.4 1.0 O B:HOH1007 2.2 43.2 1.0 O B:HOH1008 2.2 50.4 1.0 O B:HOH1009 2.3 41.9 1.0 O B:HOH1011 2.5 52.0 1.0 CG B:ASP564 3.2 47.6 1.0 OD2 B:ASP564 3.5 48.2 1.0 CD2 B:HIS567 3.6 61.7 1.0 NE2 B:HIS567 3.7 61.8 1.0 NE2 B:HIS595 3.9 53.8 1.0 NI B:NI901 4.0 50.8 1.0 O B:HOH1006 4.0 48.5 1.0 CD2 B:HIS525 4.0 68.4 1.0 OE2 B:GLU592 4.1 64.3 1.0 CD2 B:HIS595 4.3 54.2 1.0 O B:HIS563 4.4 46.7 1.0 OG1 B:THR633 4.4 49.9 1.0 NE2 B:HIS525 4.5 68.7 1.0 CB B:ASP564 4.5 48.4 1.0 CD2 B:HIS563 4.7 44.2 1.0 O B:THR633 4.7 50.9 1.0 OD2 B:ASP674 4.9 42.7 1.0 CA B:ASP564 4.9 49.1 1.0 CE1 B:HIS595 4.9 54.2 1.0 CD B:GLU592 5.0 64.7 1.0 CG B:HIS567 5.0 62.0 1.0 CE1 B:HIS567 5.0 61.2 1.0

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