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Zinc in PDB 4heu: Crystal Structure of PDE10A with A Biaryl Ether Inhibitor ((1-(3-(4- ((1H-Benzo[D]Imidazol-2-Yl)Amino)Phenoxy)Pyridin-2-Yl)Piperidin-4- Yl)Methanol)

Enzymatic activity of Crystal Structure of PDE10A with A Biaryl Ether Inhibitor ((1-(3-(4- ((1H-Benzo[D]Imidazol-2-Yl)Amino)Phenoxy)Pyridin-2-Yl)Piperidin-4- Yl)Methanol)

All present enzymatic activity of Crystal Structure of PDE10A with A Biaryl Ether Inhibitor ((1-(3-(4- ((1H-Benzo[D]Imidazol-2-Yl)Amino)Phenoxy)Pyridin-2-Yl)Piperidin-4- Yl)Methanol):
3.1.4.35;

Protein crystallography data

The structure of Crystal Structure of PDE10A with A Biaryl Ether Inhibitor ((1-(3-(4- ((1H-Benzo[D]Imidazol-2-Yl)Amino)Phenoxy)Pyridin-2-Yl)Piperidin-4- Yl)Methanol), PDB code: 4heu was solved by S.Chmait, S.Jordan, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 48.66 / 2.00
Space group F 2 3
Cell size a, b, c (Å), α, β, γ (°) 252.859, 252.859, 252.859, 90.00, 90.00, 90.00
R / Rfree (%) 18.6 / 19.9

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of PDE10A with A Biaryl Ether Inhibitor ((1-(3-(4- ((1H-Benzo[D]Imidazol-2-Yl)Amino)Phenoxy)Pyridin-2-Yl)Piperidin-4- Yl)Methanol) (pdb code 4heu). 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 A Biaryl Ether Inhibitor ((1-(3-(4- ((1H-Benzo[D]Imidazol-2-Yl)Amino)Phenoxy)Pyridin-2-Yl)Piperidin-4- Yl)Methanol), PDB code: 4heu:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in 4heu

Go back to Zinc Binding Sites List in 4heu
Zinc binding site 1 out of 4 in the Crystal Structure of PDE10A with A Biaryl Ether Inhibitor ((1-(3-(4- ((1H-Benzo[D]Imidazol-2-Yl)Amino)Phenoxy)Pyridin-2-Yl)Piperidin-4- Yl)Methanol)


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 A Biaryl Ether Inhibitor ((1-(3-(4- ((1H-Benzo[D]Imidazol-2-Yl)Amino)Phenoxy)Pyridin-2-Yl)Piperidin-4- Yl)Methanol) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1001

b:28.7
occ:1.00
 O A:HOH1275 2.1 23.5 1.0
OD2 A:ASP554 2.1 24.1 1.0
NE2 A:HIS553 2.1 24.3 1.0
OD1 A:ASP664 2.2 25.8 1.0
NE2 A:HIS519 2.2 23.8 1.0
O A:HOH1159 2.3 29.3 1.0
CD2 A:HIS553 3.0 24.0 1.0
CD2 A:HIS519 3.1 23.6 1.0
CG A:ASP664 3.1 26.0 1.0
CG A:ASP554 3.1 24.5 1.0
CE1 A:HIS553 3.2 24.0 1.0
CE1 A:HIS519 3.3 24.0 1.0
OD2 A:ASP664 3.4 27.0 1.0
OD1 A:ASP554 3.6 24.5 1.0
ZN A:ZN1002 3.6 26.1 0.7
O A:HOH1156 4.0 26.6 1.0
CD2 A:HIS515 4.1 26.5 1.0
CG A:HIS553 4.2 24.0 1.0
ND1 A:HIS553 4.3 23.9 1.0
CB A:ASP554 4.3 24.1 1.0
CG A:HIS519 4.3 23.8 1.0
ND1 A:HIS519 4.4 23.6 1.0
NE2 A:HIS515 4.4 26.8 1.0
CB A:ASP664 4.4 25.5 1.0
O A:HOH1238 4.4 42.3 1.0
O A:HOH1126 4.6 28.0 1.0
O A:HOH1153 4.6 24.9 1.0
CG2 A:VAL523 4.8 23.8 1.0
O A:ASP664 4.9 25.6 1.0
CA A:ASP664 4.9 25.4 1.0

Zinc binding site 2 out of 4 in 4heu

Go back to Zinc Binding Sites List in 4heu
Zinc binding site 2 out of 4 in the Crystal Structure of PDE10A with A Biaryl Ether Inhibitor ((1-(3-(4- ((1H-Benzo[D]Imidazol-2-Yl)Amino)Phenoxy)Pyridin-2-Yl)Piperidin-4- Yl)Methanol)


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 A Biaryl Ether Inhibitor ((1-(3-(4- ((1H-Benzo[D]Imidazol-2-Yl)Amino)Phenoxy)Pyridin-2-Yl)Piperidin-4- Yl)Methanol) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1002

b:26.1
occ:0.65
 O A:HOH1275 2.0 23.5 1.0
O A:HOH1153 2.1 24.9 1.0
OD1 A:ASP554 2.1 24.5 1.0
O A:HOH1155 2.2 27.0 1.0
O A:HOH1156 2.2 26.6 1.0
O A:HOH1152 2.3 23.0 1.0
CG A:ASP554 3.1 24.5 1.0
OD2 A:ASP554 3.4 24.1 1.0
ZN A:ZN1001 3.6 28.7 1.0
O A:HOH1238 4.0 42.3 1.0
O A:HOH1159 4.0 29.3 1.0
NE2 A:HIS585 4.0 24.9 1.0
OE2 A:GLU582 4.1 26.8 1.0
OG1 A:THR623 4.2 26.4 1.0
CD2 A:HIS553 4.2 24.0 1.0
O A:HOH1174 4.2 35.2 1.0
CD2 A:HIS585 4.3 24.6 1.0
O A:HIS553 4.3 24.3 1.0
CD2 A:HIS557 4.4 27.4 1.0
CB A:ASP554 4.5 24.1 1.0
OD2 A:ASP664 4.5 27.0 1.0
NE2 A:HIS553 4.5 24.3 1.0
O A:THR623 4.5 28.4 1.0
CD2 A:HIS515 4.6 26.5 1.0
NE2 A:HIS557 4.6 28.3 1.0
CB A:THR623 4.6 26.7 1.0
NE2 A:HIS515 4.7 26.8 1.0
CA A:ASP554 4.8 24.2 1.0
CG A:GLU582 4.9 26.1 1.0
CD A:GLU582 5.0 26.7 1.0

Zinc binding site 3 out of 4 in 4heu

Go back to Zinc Binding Sites List in 4heu
Zinc binding site 3 out of 4 in the Crystal Structure of PDE10A with A Biaryl Ether Inhibitor ((1-(3-(4- ((1H-Benzo[D]Imidazol-2-Yl)Amino)Phenoxy)Pyridin-2-Yl)Piperidin-4- Yl)Methanol)


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 A Biaryl Ether Inhibitor ((1-(3-(4- ((1H-Benzo[D]Imidazol-2-Yl)Amino)Phenoxy)Pyridin-2-Yl)Piperidin-4- Yl)Methanol) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn801

b:30.2
occ:1.00
 O B:HOH901 2.1 26.1 1.0
OD1 B:ASP664 2.1 27.3 1.0
OD2 B:ASP554 2.1 25.9 1.0
NE2 B:HIS553 2.1 23.9 1.0
NE2 B:HIS519 2.2 24.6 1.0
O B:HOH956 2.5 33.6 1.0
CD2 B:HIS553 3.0 24.1 1.0
CG B:ASP664 3.1 27.7 1.0
CD2 B:HIS519 3.1 24.6 1.0
CG B:ASP554 3.1 25.6 1.0
CE1 B:HIS553 3.2 23.8 1.0
CE1 B:HIS519 3.2 24.9 1.0
OD2 B:ASP664 3.4 28.6 1.0
OD1 B:ASP554 3.6 26.2 1.0
ZN B:ZN802 3.6 32.1 0.8
CD2 B:HIS515 4.0 28.4 1.0
O B:HOH958 4.0 28.4 1.0
CG B:HIS553 4.2 24.0 1.0
ND1 B:HIS553 4.3 23.8 1.0
CB B:ASP554 4.3 25.1 1.0
CG B:HIS519 4.3 24.7 1.0
ND1 B:HIS519 4.3 24.6 1.0
CB B:ASP664 4.4 27.3 1.0
NE2 B:HIS515 4.4 29.0 1.0
O B:HOH1081 4.5 41.8 1.0
O B:HOH957 4.6 25.9 1.0
O B:HOH943 4.6 24.6 1.0
CG2 B:VAL523 4.7 23.6 1.0
CA B:ASP664 4.9 27.0 1.0
O B:ASP664 4.9 27.0 1.0

Zinc binding site 4 out of 4 in 4heu

Go back to Zinc Binding Sites List in 4heu
Zinc binding site 4 out of 4 in the Crystal Structure of PDE10A with A Biaryl Ether Inhibitor ((1-(3-(4- ((1H-Benzo[D]Imidazol-2-Yl)Amino)Phenoxy)Pyridin-2-Yl)Piperidin-4- Yl)Methanol)


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 A Biaryl Ether Inhibitor ((1-(3-(4- ((1H-Benzo[D]Imidazol-2-Yl)Amino)Phenoxy)Pyridin-2-Yl)Piperidin-4- Yl)Methanol) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn802

b:32.1
occ:0.80
 O B:HOH901 2.0 26.1 1.0
O B:HOH943 2.1 24.6 1.0
OD1 B:ASP554 2.1 26.2 1.0
O B:HOH958 2.2 28.4 1.0
O B:HOH959 2.2 28.5 1.0
O B:HOH955 2.3 25.8 1.0
CG B:ASP554 3.1 25.6 1.0
OD2 B:ASP554 3.4 25.9 1.0
ZN B:ZN801 3.6 30.2 1.0
O B:HOH1081 4.0 41.8 1.0
OE2 B:GLU582 4.1 29.6 1.0
NE2 B:HIS585 4.1 27.3 1.0
O B:HOH956 4.1 33.6 1.0
OG1 B:THR623 4.2 27.0 1.0
CD2 B:HIS553 4.2 24.1 1.0
O B:HOH1107 4.3 39.9 1.0
CD2 B:HIS557 4.3 29.3 1.0
CD2 B:HIS585 4.3 26.9 1.0
O B:HIS553 4.4 24.8 1.0
OD2 B:ASP664 4.4 28.6 1.0
CB B:ASP554 4.5 25.1 1.0
NE2 B:HIS557 4.5 29.5 1.0
NE2 B:HIS553 4.5 23.9 1.0
O B:THR623 4.5 27.9 1.0
CD2 B:HIS515 4.6 28.4 1.0
CB B:THR623 4.6 26.7 1.0
NE2 B:HIS515 4.7 29.0 1.0
CA B:ASP554 4.8 25.0 1.0
OD1 B:ASP664 4.9 27.3 1.0
CD B:GLU582 5.0 29.4 1.0
CG B:GLU582 5.0 28.6 1.0

Reference:

R.M.Rzasa, E.Hu, S.Rumfelt, N.Chen, K.L.Andrews, S.Chmait, J.R.Falsey, W.Zhong, A.D.Jones, A.Porter, S.W.Louie, X.Zhao, J.J.Treanor, J.R.Allen. Discovery of Selective Biaryl Ethers As PDE10A Inhibitors: Improvement in Potency and Mitigation of Pgp-Mediated Efflux. Bioorg.Med.Chem.Lett. V. 22 7371 2012.
ISSN: ISSN 0960-894X
PubMed: 23149228
DOI: 10.1016/J.BMCL.2012.10.078
Page generated: Sun Oct 27 00:02:13 2024

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