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Zinc in PDB 5ede: Human PDE10A in Complex with 1-(4-Chloro-Phenyl)-3-Methyl-1H-Thieno[2, 3-C]Pyrazole-5-Carboxylic Acid (Tetrahydro-Furan-2-Ylmethyl)-Amide at 2.2A

Enzymatic activity of Human PDE10A in Complex with 1-(4-Chloro-Phenyl)-3-Methyl-1H-Thieno[2, 3-C]Pyrazole-5-Carboxylic Acid (Tetrahydro-Furan-2-Ylmethyl)-Amide at 2.2A

All present enzymatic activity of Human PDE10A in Complex with 1-(4-Chloro-Phenyl)-3-Methyl-1H-Thieno[2, 3-C]Pyrazole-5-Carboxylic Acid (Tetrahydro-Furan-2-Ylmethyl)-Amide at 2.2A:
3.1.4.17; 3.1.4.35;

Protein crystallography data

The structure of Human PDE10A in Complex with 1-(4-Chloro-Phenyl)-3-Methyl-1H-Thieno[2, 3-C]Pyrazole-5-Carboxylic Acid (Tetrahydro-Furan-2-Ylmethyl)-Amide at 2.2A, PDB code: 5ede was solved by C.Joseph, M.G.Rudolph, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 43.73 / 2.20
Space group H 3
Cell size a, b, c (Å), α, β, γ (°) 135.610, 135.610, 235.660, 90.00, 90.00, 120.00
R / Rfree (%) 18.4 / 24.2

Other elements in 5ede:

The structure of Human PDE10A in Complex with 1-(4-Chloro-Phenyl)-3-Methyl-1H-Thieno[2, 3-C]Pyrazole-5-Carboxylic Acid (Tetrahydro-Furan-2-Ylmethyl)-Amide at 2.2A also contains other interesting chemical elements:

Magnesium (Mg) 4 atoms
Chlorine (Cl) 4 atoms

Zinc Binding Sites:

The binding sites of Zinc atom in the Human PDE10A in Complex with 1-(4-Chloro-Phenyl)-3-Methyl-1H-Thieno[2, 3-C]Pyrazole-5-Carboxylic Acid (Tetrahydro-Furan-2-Ylmethyl)-Amide at 2.2A (pdb code 5ede). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the Human PDE10A in Complex with 1-(4-Chloro-Phenyl)-3-Methyl-1H-Thieno[2, 3-C]Pyrazole-5-Carboxylic Acid (Tetrahydro-Furan-2-Ylmethyl)-Amide at 2.2A, PDB code: 5ede:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in 5ede

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Zinc binding site 1 out of 4 in the Human PDE10A in Complex with 1-(4-Chloro-Phenyl)-3-Methyl-1H-Thieno[2, 3-C]Pyrazole-5-Carboxylic Acid (Tetrahydro-Furan-2-Ylmethyl)-Amide at 2.2A


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Human PDE10A in Complex with 1-(4-Chloro-Phenyl)-3-Methyl-1H-Thieno[2, 3-C]Pyrazole-5-Carboxylic Acid (Tetrahydro-Furan-2-Ylmethyl)-Amide at 2.2A within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn801

b:28.4
occ:1.00
 NE2 A:HIS563 2.1 18.9 1.0
NE2 A:HIS529 2.1 29.0 1.0
O A:HOH970 2.2 30.3 1.0
OD1 A:ASP674 2.2 27.8 1.0
O A:HOH1016 2.2 27.2 1.0
OD2 A:ASP564 2.3 24.1 1.0
CD2 A:HIS563 3.0 16.9 1.0
CE1 A:HIS563 3.1 22.5 1.0
CD2 A:HIS529 3.1 26.2 1.0
CE1 A:HIS529 3.1 28.0 1.0
CG A:ASP674 3.2 27.9 1.0
CG A:ASP564 3.2 22.8 1.0
OD2 A:ASP674 3.6 31.5 1.0
OD1 A:ASP564 3.7 21.9 1.0
MG A:MG802 3.8 25.4 1.0
CG A:HIS563 4.1 18.2 1.0
ND1 A:HIS563 4.1 14.7 1.0
O A:HOH971 4.2 29.3 1.0
CD2 A:HIS525 4.2 24.0 1.0
ND1 A:HIS529 4.2 25.6 1.0
CG A:HIS529 4.2 25.1 1.0
O A:HOH1048 4.4 21.9 1.0
CB A:ASP564 4.4 20.4 1.0
CB A:ASP674 4.5 26.5 1.0
O A:HOH931 4.5 13.6 1.0
NE2 A:HIS525 4.5 21.3 1.0
CG2 A:VAL533 4.6 17.7 1.0
O A:ASP674 4.8 26.1 1.0
CA A:ASP674 4.9 25.9 1.0

Zinc binding site 2 out of 4 in 5ede

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Zinc binding site 2 out of 4 in the Human PDE10A in Complex with 1-(4-Chloro-Phenyl)-3-Methyl-1H-Thieno[2, 3-C]Pyrazole-5-Carboxylic Acid (Tetrahydro-Furan-2-Ylmethyl)-Amide at 2.2A


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Human PDE10A in Complex with 1-(4-Chloro-Phenyl)-3-Methyl-1H-Thieno[2, 3-C]Pyrazole-5-Carboxylic Acid (Tetrahydro-Furan-2-Ylmethyl)-Amide at 2.2A within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn801

b:24.2
occ:1.00
 NE2 B:HIS563 2.1 17.5 1.0
O B:HOH919 2.1 12.2 1.0
OD1 B:ASP674 2.2 12.3 1.0
OD2 B:ASP564 2.3 16.4 1.0
NE2 B:HIS529 2.3 23.2 1.0
O B:HOH1010 2.5 29.7 1.0
CD2 B:HIS563 3.0 13.2 1.0
CG B:ASP674 3.1 21.4 1.0
CG B:ASP564 3.1 22.7 1.0
CE1 B:HIS563 3.2 20.7 1.0
CE1 B:HIS529 3.2 24.9 1.0
OD2 B:ASP674 3.2 16.0 1.0
CD2 B:HIS529 3.3 21.7 1.0
OD1 B:ASP564 3.5 25.2 1.0
MG B:MG802 3.7 12.3 1.0
O B:HOH1040 4.0 14.2 1.0
CD2 B:HIS525 4.1 23.9 1.0
O B:HOH992 4.1 30.6 1.0
CG B:HIS563 4.1 16.2 1.0
ND1 B:HIS563 4.2 16.9 1.0
CB B:ASP564 4.3 17.2 1.0
ND1 B:HIS529 4.4 16.7 1.0
CG B:HIS529 4.4 20.4 1.0
NE2 B:HIS525 4.4 28.4 1.0
O B:HOH1054 4.5 41.7 1.0
CB B:ASP674 4.5 19.8 1.0
O B:HOH977 4.5 13.9 1.0
CG2 B:VAL533 4.8 21.0 1.0
CA B:ASP674 5.0 20.3 1.0

Zinc binding site 3 out of 4 in 5ede

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Zinc binding site 3 out of 4 in the Human PDE10A in Complex with 1-(4-Chloro-Phenyl)-3-Methyl-1H-Thieno[2, 3-C]Pyrazole-5-Carboxylic Acid (Tetrahydro-Furan-2-Ylmethyl)-Amide at 2.2A


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Human PDE10A in Complex with 1-(4-Chloro-Phenyl)-3-Methyl-1H-Thieno[2, 3-C]Pyrazole-5-Carboxylic Acid (Tetrahydro-Furan-2-Ylmethyl)-Amide at 2.2A within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn801

b:26.1
occ:1.00
 NE2 C:HIS529 2.1 24.4 1.0
OD2 C:ASP564 2.2 17.8 1.0
O C:HOH950 2.2 19.6 1.0
OD1 C:ASP674 2.2 19.6 1.0
NE2 C:HIS563 2.3 24.5 1.0
O C:HOH963 2.6 37.2 1.0
CD2 C:HIS563 3.0 19.4 1.0
CD2 C:HIS529 3.1 24.2 1.0
CE1 C:HIS529 3.1 23.4 1.0
CG C:ASP674 3.1 24.5 1.0
CG C:ASP564 3.2 19.9 1.0
CE1 C:HIS563 3.3 25.5 1.0
OD2 C:ASP674 3.4 25.7 1.0
OD1 C:ASP564 3.7 26.0 1.0
MG C:MG802 3.9 22.6 1.0
CD2 C:HIS525 4.0 26.3 1.0
O C:HOH1036 4.2 23.4 1.0
ND1 C:HIS529 4.2 21.4 1.0
CG C:HIS529 4.2 20.7 1.0
CG C:HIS563 4.2 21.7 1.0
O C:HOH1031 4.3 26.9 1.0
ND1 C:HIS563 4.3 23.8 1.0
NE2 C:HIS525 4.4 26.6 1.0
CB C:ASP564 4.4 17.4 1.0
CB C:ASP674 4.5 25.7 1.0
O C:HOH956 4.6 18.9 1.0
O C:HOH1083 4.7 50.6 1.0
CG2 C:VAL533 4.8 18.3 1.0
CA C:ASP674 4.8 24.9 1.0
O C:ASP674 4.9 25.4 1.0

Zinc binding site 4 out of 4 in 5ede

Go back to Zinc Binding Sites List in 5ede
Zinc binding site 4 out of 4 in the Human PDE10A in Complex with 1-(4-Chloro-Phenyl)-3-Methyl-1H-Thieno[2, 3-C]Pyrazole-5-Carboxylic Acid (Tetrahydro-Furan-2-Ylmethyl)-Amide at 2.2A


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Human PDE10A in Complex with 1-(4-Chloro-Phenyl)-3-Methyl-1H-Thieno[2, 3-C]Pyrazole-5-Carboxylic Acid (Tetrahydro-Furan-2-Ylmethyl)-Amide at 2.2A within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn801

b:33.4
occ:1.00
 O D:HOH939 2.0 17.9 1.0
OD1 D:ASP674 2.2 24.0 1.0
NE2 D:HIS563 2.2 22.1 1.0
O D:HOH955 2.2 47.0 1.0
NE2 D:HIS529 2.2 29.6 1.0
OD2 D:ASP564 2.4 27.3 1.0
CD2 D:HIS563 3.0 22.4 1.0
CG D:ASP674 3.1 33.0 1.0
CE1 D:HIS529 3.2 27.1 1.0
CD2 D:HIS529 3.2 31.5 1.0
OD2 D:ASP674 3.3 32.9 1.0
CG D:ASP564 3.3 30.4 1.0
CE1 D:HIS563 3.3 26.9 1.0
OD1 D:ASP564 3.8 28.3 1.0
O D:HOH948 3.9 29.2 1.0
MG D:MG802 3.9 31.0 1.0
CD2 D:HIS525 4.2 32.2 1.0
CG D:HIS563 4.2 24.3 1.0
O D:HOH993 4.3 23.3 1.0
ND1 D:HIS529 4.3 30.0 1.0
ND1 D:HIS563 4.3 21.2 1.0
CG D:HIS529 4.4 27.1 1.0
CB D:ASP564 4.4 27.8 1.0
CB D:ASP674 4.5 31.8 1.0
NE2 D:HIS525 4.5 34.7 1.0
O D:HOH905 4.7 27.6 1.0
O D:ASP674 4.7 32.4 1.0
CG2 D:VAL533 4.7 24.4 1.0
CA D:ASP674 4.9 31.5 1.0
O D:HOH934 4.9 26.1 1.0

Reference:

B.Kuhn, W.Guba, J.Hert, D.Banner, C.Bissantz, S.Ceccarelli, W.Haap, M.Korner, A.Kuglstatter, C.Lerner, P.Mattei, W.Neidhart, E.Pinard, M.G.Rudolph, T.Schulz-Gasch, T.Woltering, M.Stahl. A Real-World Perspective on Molecular Design. J.Med.Chem. V. 59 4087 2016.
ISSN: ISSN 0022-2623
PubMed: 26878596
DOI: 10.1021/ACS.JMEDCHEM.5B01875
Page generated: Sun Oct 27 15:08:59 2024

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