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Zinc in PDB 5sf4: Crystal Structure of Human Phosphodiesterase 10 in Complex with 6- Cyclopropyl-N-[2-[2-(Dimethylamino)Ethyl]-5-Pyridin-2-Ylpyrazol-3- Yl]-3-(Pyrimidin-5-Ylamino)Pyridine-2-Carboxamide

Enzymatic activity of Crystal Structure of Human Phosphodiesterase 10 in Complex with 6- Cyclopropyl-N-[2-[2-(Dimethylamino)Ethyl]-5-Pyridin-2-Ylpyrazol-3- Yl]-3-(Pyrimidin-5-Ylamino)Pyridine-2-Carboxamide

All present enzymatic activity of Crystal Structure of Human Phosphodiesterase 10 in Complex with 6- Cyclopropyl-N-[2-[2-(Dimethylamino)Ethyl]-5-Pyridin-2-Ylpyrazol-3- Yl]-3-(Pyrimidin-5-Ylamino)Pyridine-2-Carboxamide:
3.1.4.17;

Protein crystallography data

The structure of Crystal Structure of Human Phosphodiesterase 10 in Complex with 6- Cyclopropyl-N-[2-[2-(Dimethylamino)Ethyl]-5-Pyridin-2-Ylpyrazol-3- Yl]-3-(Pyrimidin-5-Ylamino)Pyridine-2-Carboxamide, PDB code: 5sf4 was solved by C.Joseph, K.Groebke-Zbinden, J.Benz, D.Schlatter, M.G.Rudolph, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 43.31 / 2.25
Space group H 3
Cell size a, b, c (Å), α, β, γ (°) 134.65, 134.65, 234.099, 90, 90, 120
R / Rfree (%) 18.5 / 23.5

Other elements in 5sf4:

The structure of Crystal Structure of Human Phosphodiesterase 10 in Complex with 6- Cyclopropyl-N-[2-[2-(Dimethylamino)Ethyl]-5-Pyridin-2-Ylpyrazol-3- Yl]-3-(Pyrimidin-5-Ylamino)Pyridine-2-Carboxamide also contains other interesting chemical elements:

Magnesium (Mg) 4 atoms

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of Human Phosphodiesterase 10 in Complex with 6- Cyclopropyl-N-[2-[2-(Dimethylamino)Ethyl]-5-Pyridin-2-Ylpyrazol-3- Yl]-3-(Pyrimidin-5-Ylamino)Pyridine-2-Carboxamide (pdb code 5sf4). 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 Human Phosphodiesterase 10 in Complex with 6- Cyclopropyl-N-[2-[2-(Dimethylamino)Ethyl]-5-Pyridin-2-Ylpyrazol-3- Yl]-3-(Pyrimidin-5-Ylamino)Pyridine-2-Carboxamide, PDB code: 5sf4:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in 5sf4

Go back to Zinc Binding Sites List in 5sf4
Zinc binding site 1 out of 4 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with 6- Cyclopropyl-N-[2-[2-(Dimethylamino)Ethyl]-5-Pyridin-2-Ylpyrazol-3- Yl]-3-(Pyrimidin-5-Ylamino)Pyridine-2-Carboxamide


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 Human Phosphodiesterase 10 in Complex with 6- Cyclopropyl-N-[2-[2-(Dimethylamino)Ethyl]-5-Pyridin-2-Ylpyrazol-3- Yl]-3-(Pyrimidin-5-Ylamino)Pyridine-2-Carboxamide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn801

b:33.0
occ:1.00
 O A:HOH983 2.0 23.0 1.0
OD2 A:ASP564 2.1 30.6 1.0
NE2 A:HIS563 2.1 22.9 1.0
OD1 A:ASP674 2.1 30.6 1.0
NE2 A:HIS529 2.2 26.4 1.0
O A:HOH962 2.7 36.0 1.0
CD2 A:HIS563 3.0 23.4 1.0
CG A:ASP564 3.1 28.4 1.0
CG A:ASP674 3.1 29.6 1.0
CE1 A:HIS529 3.1 26.2 1.0
CD2 A:HIS529 3.1 26.3 1.0
CE1 A:HIS563 3.2 25.3 1.0
OD2 A:ASP674 3.4 36.3 1.0
OD1 A:ASP564 3.5 26.4 1.0
MG A:MG802 3.7 22.1 1.0
O A:HOH1001 4.1 23.6 1.0
CD2 A:HIS525 4.1 24.9 1.0
CG A:HIS563 4.2 24.9 1.0
ND1 A:HIS529 4.2 26.3 1.0
CB A:ASP564 4.2 26.7 1.0
CG A:HIS529 4.3 25.6 1.0
ND1 A:HIS563 4.3 23.9 1.0
O A:HOH972 4.4 34.6 1.0
CB A:ASP674 4.4 27.4 1.0
NE2 A:HIS525 4.5 25.1 1.0
O A:HOH985 4.5 52.8 1.0
O A:HOH913 4.5 24.9 1.0
CG2 A:VAL533 4.8 25.6 1.0
O A:ASP674 4.8 28.8 1.0
CA A:ASP674 4.9 27.1 1.0
O A:HOH935 4.9 27.5 1.0

Zinc binding site 2 out of 4 in 5sf4

Go back to Zinc Binding Sites List in 5sf4
Zinc binding site 2 out of 4 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with 6- Cyclopropyl-N-[2-[2-(Dimethylamino)Ethyl]-5-Pyridin-2-Ylpyrazol-3- Yl]-3-(Pyrimidin-5-Ylamino)Pyridine-2-Carboxamide


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 Human Phosphodiesterase 10 in Complex with 6- Cyclopropyl-N-[2-[2-(Dimethylamino)Ethyl]-5-Pyridin-2-Ylpyrazol-3- Yl]-3-(Pyrimidin-5-Ylamino)Pyridine-2-Carboxamide within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn801

b:32.4
occ:1.00
 O B:HOH950 2.1 19.8 1.0
NE2 B:HIS563 2.1 22.3 1.0
OD1 B:ASP674 2.1 27.5 1.0
NE2 B:HIS529 2.1 23.9 1.0
OD2 B:ASP564 2.2 24.8 1.0
O B:HOH936 2.5 32.8 1.0
CD2 B:HIS563 3.0 23.7 1.0
CG B:ASP674 3.0 27.4 1.0
CD2 B:HIS529 3.1 25.7 1.0
CE1 B:HIS563 3.1 22.7 1.0
CG B:ASP564 3.1 24.7 1.0
CE1 B:HIS529 3.2 25.4 1.0
OD2 B:ASP674 3.3 31.4 1.0
OD1 B:ASP564 3.6 24.8 1.0
MG B:MG802 3.9 20.1 1.0
O B:HOH998 4.0 21.9 1.0
CD2 B:HIS525 4.1 29.4 1.0
O B:HOH941 4.1 33.2 1.0
CG B:HIS563 4.2 24.0 1.0
ND1 B:HIS563 4.2 22.6 1.0
CG B:HIS529 4.3 24.4 1.0
ND1 B:HIS529 4.3 25.0 1.0
CB B:ASP564 4.3 24.6 1.0
NE2 B:HIS525 4.4 29.0 1.0
CB B:ASP674 4.4 27.5 1.0
O B:HOH1012 4.4 48.9 1.0
O B:HOH937 4.6 23.5 1.0
CA B:ASP674 4.8 26.3 1.0
O B:ASP674 4.8 27.3 1.0
CG2 B:VAL533 4.9 23.9 1.0

Zinc binding site 3 out of 4 in 5sf4

Go back to Zinc Binding Sites List in 5sf4
Zinc binding site 3 out of 4 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with 6- Cyclopropyl-N-[2-[2-(Dimethylamino)Ethyl]-5-Pyridin-2-Ylpyrazol-3- Yl]-3-(Pyrimidin-5-Ylamino)Pyridine-2-Carboxamide


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 Human Phosphodiesterase 10 in Complex with 6- Cyclopropyl-N-[2-[2-(Dimethylamino)Ethyl]-5-Pyridin-2-Ylpyrazol-3- Yl]-3-(Pyrimidin-5-Ylamino)Pyridine-2-Carboxamide within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn801

b:31.9
occ:1.00
 O C:HOH938 1.8 20.7 1.0
OD1 C:ASP674 2.1 28.3 1.0
OD2 C:ASP564 2.1 23.9 1.0
NE2 C:HIS529 2.1 30.3 1.0
NE2 C:HIS563 2.1 24.0 1.0
O C:HOH971 2.3 35.0 1.0
CD2 C:HIS563 3.0 22.8 1.0
CG C:ASP674 3.0 27.1 1.0
CD2 C:HIS529 3.1 29.6 1.0
CE1 C:HIS529 3.1 32.1 1.0
CG C:ASP564 3.2 25.3 1.0
CE1 C:HIS563 3.3 24.6 1.0
OD2 C:ASP674 3.3 27.4 1.0
OD1 C:ASP564 3.7 24.8 1.0
MG C:MG802 3.8 25.2 1.0
O C:HOH1005 4.1 31.4 1.0
CD2 C:HIS525 4.1 32.8 1.0
CG C:HIS563 4.2 23.9 1.0
ND1 C:HIS529 4.2 29.5 1.0
CG C:HIS529 4.3 29.0 1.0
ND1 C:HIS563 4.3 23.4 1.0
O C:HOH988 4.3 40.2 1.0
CB C:ASP564 4.3 24.8 1.0
CB C:ASP674 4.4 27.5 1.0
NE2 C:HIS525 4.4 31.9 1.0
O C:HOH928 4.5 23.8 1.0
O C:HOH1004 4.6 51.4 1.0
CG2 C:VAL533 4.7 26.1 1.0
O C:ASP674 4.7 28.1 1.0
CA C:ASP674 4.7 27.8 1.0

Zinc binding site 4 out of 4 in 5sf4

Go back to Zinc Binding Sites List in 5sf4
Zinc binding site 4 out of 4 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with 6- Cyclopropyl-N-[2-[2-(Dimethylamino)Ethyl]-5-Pyridin-2-Ylpyrazol-3- Yl]-3-(Pyrimidin-5-Ylamino)Pyridine-2-Carboxamide


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 Human Phosphodiesterase 10 in Complex with 6- Cyclopropyl-N-[2-[2-(Dimethylamino)Ethyl]-5-Pyridin-2-Ylpyrazol-3- Yl]-3-(Pyrimidin-5-Ylamino)Pyridine-2-Carboxamide within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn801

b:46.0
occ:1.00
 O D:HOH936 2.0 27.1 1.0
NE2 D:HIS563 2.1 34.3 1.0
OD2 D:ASP564 2.1 47.4 1.0
OD1 D:ASP674 2.2 41.2 1.0
NE2 D:HIS529 2.3 43.2 1.0
O D:HOH943 2.6 41.3 1.0
CD2 D:HIS563 3.0 35.6 1.0
CG D:ASP674 3.1 40.5 1.0
CD2 D:HIS529 3.1 39.6 1.0
CG D:ASP564 3.1 37.8 1.0
CE1 D:HIS563 3.2 36.3 1.0
CE1 D:HIS529 3.4 42.3 1.0
OD2 D:ASP674 3.4 44.2 1.0
MG D:MG802 3.7 38.3 1.0
OD1 D:ASP564 3.7 36.0 1.0
O D:HOH948 4.0 47.3 1.0
O D:HOH960 4.1 33.0 1.0
CG D:HIS563 4.1 34.8 1.0
CB D:ASP564 4.2 38.1 1.0
ND1 D:HIS563 4.2 33.9 1.0
O D:HOH931 4.2 34.5 1.0
CD2 D:HIS525 4.3 44.3 1.0
CG D:HIS529 4.3 36.5 1.0
ND1 D:HIS529 4.4 42.3 1.0
CB D:ASP674 4.5 42.9 1.0
CG2 D:VAL533 4.7 47.0 1.0
NE2 D:HIS525 4.7 42.1 1.0
O D:ASP674 4.7 40.8 1.0
CA D:ASP674 4.8 39.9 1.0

Reference:

A.Tosstorff, M.G.Rudolph, J.C.Cole, M.Reutlinger, C.Kramer, H.Schaffhauser, A.Nilly, A.Flohr, B.Kuhn. A High Quality, Industrial Data Set For Binding Affinity Prediction: Performance Comparison in Different Early Drug Discovery Scenarios. J.Comput.Aided Mol.Des. V. 36 753 2022.
ISSN: ESSN 1573-4951
PubMed: 36153472
DOI: 10.1007/S10822-022-00478-X
Page generated: Mon Oct 28 04:50:43 2024

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