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Zinc in PDB 4phw: Crystal Structure of PDE10A with 1H-Benzimidazol-2-Yl(4-((3- (Tetrahydro-2H-Pyran-4-Yl)-2-Pyridinyl)Oxy)Phenyl)Methanone

Enzymatic activity of Crystal Structure of PDE10A with 1H-Benzimidazol-2-Yl(4-((3- (Tetrahydro-2H-Pyran-4-Yl)-2-Pyridinyl)Oxy)Phenyl)Methanone

All present enzymatic activity of Crystal Structure of PDE10A with 1H-Benzimidazol-2-Yl(4-((3- (Tetrahydro-2H-Pyran-4-Yl)-2-Pyridinyl)Oxy)Phenyl)Methanone:
3.1.4.17; 3.1.4.35;

Protein crystallography data

The structure of Crystal Structure of PDE10A with 1H-Benzimidazol-2-Yl(4-((3- (Tetrahydro-2H-Pyran-4-Yl)-2-Pyridinyl)Oxy)Phenyl)Methanone, PDB code: 4phw was solved by S.Chmait, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 30.00 / 2.50
Space group F 2 3
Cell size a, b, c (Å), α, β, γ (°) 253.340, 253.340, 253.340, 90.00, 90.00, 90.00
R / Rfree (%) 16 / 18

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of PDE10A with 1H-Benzimidazol-2-Yl(4-((3- (Tetrahydro-2H-Pyran-4-Yl)-2-Pyridinyl)Oxy)Phenyl)Methanone (pdb code 4phw). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the Crystal Structure of PDE10A with 1H-Benzimidazol-2-Yl(4-((3- (Tetrahydro-2H-Pyran-4-Yl)-2-Pyridinyl)Oxy)Phenyl)Methanone, PDB code: 4phw:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in 4phw

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Zinc binding site 1 out of 4 in the Crystal Structure of PDE10A with 1H-Benzimidazol-2-Yl(4-((3- (Tetrahydro-2H-Pyran-4-Yl)-2-Pyridinyl)Oxy)Phenyl)Methanone


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 PDE10A with 1H-Benzimidazol-2-Yl(4-((3- (Tetrahydro-2H-Pyran-4-Yl)-2-Pyridinyl)Oxy)Phenyl)Methanone within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn801

b:47.6
occ:1.00
 OD2 A:ASP554 2.2 39.8 1.0
NE2 A:HIS553 2.2 33.6 1.0
OD1 A:ASP664 2.4 39.7 1.0
NE2 A:HIS519 2.5 39.1 1.0
CD2 A:HIS553 3.1 32.9 1.0
CG A:ASP554 3.1 35.9 1.0
CG A:ASP664 3.1 37.6 1.0
OD2 A:ASP664 3.3 38.5 1.0
CE1 A:HIS553 3.3 33.6 1.0
CD2 A:HIS519 3.3 37.8 1.0
OD1 A:ASP554 3.5 37.7 1.0
CE1 A:HIS519 3.5 39.6 1.0
ZN A:ZN802 3.6 62.2 1.0
O A:HOH965 3.8 62.1 1.0
O A:HOH961 4.1 39.1 1.0
CD2 A:HIS515 4.1 41.6 1.0
O A:HOH935 4.1 38.1 1.0
CG A:HIS553 4.3 33.3 1.0
CB A:ASP554 4.3 35.8 1.0
ND1 A:HIS553 4.3 33.2 1.0
CG A:HIS519 4.5 38.4 1.0
CB A:ASP664 4.5 38.2 1.0
NE2 A:HIS515 4.6 42.5 1.0
ND1 A:HIS519 4.6 40.0 1.0
O A:HOH958 4.8 43.1 1.0
CG2 A:VAL523 4.8 36.5 1.0
CA A:ASP664 5.0 38.3 1.0
O A:ASP664 5.0 37.3 1.0

Zinc binding site 2 out of 4 in 4phw

Go back to Zinc Binding Sites List in 4phw
Zinc binding site 2 out of 4 in the Crystal Structure of PDE10A with 1H-Benzimidazol-2-Yl(4-((3- (Tetrahydro-2H-Pyran-4-Yl)-2-Pyridinyl)Oxy)Phenyl)Methanone


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 PDE10A with 1H-Benzimidazol-2-Yl(4-((3- (Tetrahydro-2H-Pyran-4-Yl)-2-Pyridinyl)Oxy)Phenyl)Methanone within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn802

b:62.2
occ:1.00
 O A:HOH961 2.2 39.1 1.0
OD1 A:ASP554 2.2 37.7 1.0
O A:HOH958 2.2 43.1 1.0
O A:HOH960 2.5 39.4 1.0
O A:HOH957 2.5 38.4 1.0
CG A:ASP554 3.2 35.9 1.0
OD2 A:ASP554 3.4 39.8 1.0
ZN A:ZN801 3.6 47.6 1.0
O A:HOH965 4.0 62.1 1.0
NE2 A:HIS585 4.2 35.1 1.0
OG1 A:THR623 4.2 34.6 1.0
OE2 A:GLU582 4.2 38.3 1.0
CD2 A:HIS553 4.2 32.9 1.0
OD2 A:ASP664 4.3 38.5 1.0
O A:HIS553 4.3 31.9 1.0
CD2 A:HIS557 4.5 41.8 1.0
CD2 A:HIS585 4.5 34.3 1.0
CB A:ASP554 4.5 35.8 1.0
O A:THR623 4.5 36.1 1.0
NE2 A:HIS553 4.6 33.6 1.0
CD2 A:HIS515 4.6 41.6 1.0
CB A:THR623 4.6 33.6 1.0
NE2 A:HIS515 4.7 42.5 1.0
NE2 A:HIS557 4.7 42.1 1.0
CA A:ASP554 4.8 36.0 1.0

Zinc binding site 3 out of 4 in 4phw

Go back to Zinc Binding Sites List in 4phw
Zinc binding site 3 out of 4 in the Crystal Structure of PDE10A with 1H-Benzimidazol-2-Yl(4-((3- (Tetrahydro-2H-Pyran-4-Yl)-2-Pyridinyl)Oxy)Phenyl)Methanone


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Crystal Structure of PDE10A with 1H-Benzimidazol-2-Yl(4-((3- (Tetrahydro-2H-Pyran-4-Yl)-2-Pyridinyl)Oxy)Phenyl)Methanone within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn801

b:44.6
occ:1.00
 OD1 B:ASP664 2.1 40.4 1.0
O B:HOH912 2.2 43.8 1.0
OD2 B:ASP554 2.2 32.4 1.0
NE2 B:HIS553 2.3 31.1 1.0
NE2 B:HIS519 2.3 32.8 1.0
O B:HOH963 2.7 44.2 1.0
CG B:ASP664 3.0 39.3 1.0
CG B:ASP554 3.1 32.9 1.0
CE1 B:HIS519 3.2 32.6 1.0
CD2 B:HIS553 3.2 30.8 1.0
OD2 B:ASP664 3.2 39.1 1.0
CE1 B:HIS553 3.3 31.4 1.0
CD2 B:HIS519 3.4 31.8 1.0
OD1 B:ASP554 3.5 33.3 1.0
ZN B:ZN802 3.7 54.9 1.0
O B:HOH965 4.0 39.5 1.0
CD2 B:HIS515 4.1 39.9 1.0
O B:HOH964 4.2 43.9 1.0
CB B:ASP554 4.3 33.0 1.0
CG B:HIS553 4.3 30.9 1.0
ND1 B:HIS553 4.4 31.0 1.0
ND1 B:HIS519 4.4 33.1 1.0
CB B:ASP664 4.4 39.2 1.0
CG B:HIS519 4.5 31.5 1.0
NE2 B:HIS515 4.5 40.9 1.0
O B:HOH951 4.7 26.2 1.0
CG2 B:VAL523 4.9 35.1 1.0
CA B:ASP664 4.9 39.0 1.0
O B:ASP664 5.0 40.6 1.0

Zinc binding site 4 out of 4 in 4phw

Go back to Zinc Binding Sites List in 4phw
Zinc binding site 4 out of 4 in the Crystal Structure of PDE10A with 1H-Benzimidazol-2-Yl(4-((3- (Tetrahydro-2H-Pyran-4-Yl)-2-Pyridinyl)Oxy)Phenyl)Methanone


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Crystal Structure of PDE10A with 1H-Benzimidazol-2-Yl(4-((3- (Tetrahydro-2H-Pyran-4-Yl)-2-Pyridinyl)Oxy)Phenyl)Methanone within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn802

b:54.9
occ:1.00
 O B:HOH912 2.1 43.8 1.0
OD1 B:ASP554 2.2 33.3 1.0
O B:HOH951 2.2 26.2 1.0
O B:HOH965 2.3 39.5 1.0
O B:HOH961 2.4 38.0 1.0
O B:HOH966 2.5 31.9 1.0
CG B:ASP554 3.1 32.9 1.0
OD2 B:ASP554 3.4 32.4 1.0
ZN B:ZN801 3.7 44.6 1.0
O B:HOH963 3.9 44.2 1.0
OE2 B:GLU582 3.9 37.6 1.0
NE2 B:HIS585 4.0 35.9 1.0
OG1 B:THR623 4.2 40.4 1.0
CD2 B:HIS585 4.4 35.6 1.0
O B:HIS553 4.4 31.5 1.0
CD2 B:HIS553 4.4 30.8 1.0
OD2 B:ASP664 4.5 39.1 1.0
O B:HOH962 4.5 45.9 1.0
CB B:ASP554 4.5 33.0 1.0
CD2 B:HIS557 4.5 41.9 1.0
NE2 B:HIS557 4.6 41.4 1.0
CB B:THR623 4.7 39.3 1.0
O B:THR623 4.7 37.6 1.0
NE2 B:HIS553 4.7 31.1 1.0
CD2 B:HIS515 4.8 39.9 1.0
NE2 B:HIS515 4.8 40.9 1.0
CA B:ASP554 4.9 33.0 1.0
CD B:GLU582 4.9 37.5 1.0

Reference:

E.Hu, N.Chen, M.P.Bourbeau, P.E.Harrington, K.Biswas, R.K.Kunz, K.L.Andrews, S.Chmait, X.Zhao, C.Davis, J.Ma, J.Shi, D.Lester-Zeiner, J.Danao, J.Able, M.Cueva, S.Talreja, T.Kornecook, H.Chen, A.Porter, R.Hungate, J.Treanor, J.R.Allen. Discovery of Clinical Candidate 1-(4-(3-(4-(1H-Benzo[D]Imidazole-2-Carbonyl)Phenoxy) Pyrazin-2-Yl)Piperidin-1-Yl)Ethanone (Amg 579), A Potent, Selective, and Efficacious Inhibitor of Phosphodiesterase 10A (PDE10A). J.Med.Chem. V. 57 6632 2014.
ISSN: ISSN 0022-2623
PubMed: 25062128
DOI: 10.1021/JM500713J
Page generated: Sun Oct 27 05:52:53 2024

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