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Zinc in PDB 5sfk: Crystal Structure of Human Phosphodiesterase 10 in Complex with 6- Cyclopropyl-3-(Pyrimidin-5-Ylamino)-N-[1-(2,2,2-Trifluoroethyl) Pyrazol-3-Yl]Pyridine-2-Carboxamide

Enzymatic activity of Crystal Structure of Human Phosphodiesterase 10 in Complex with 6- Cyclopropyl-3-(Pyrimidin-5-Ylamino)-N-[1-(2,2,2-Trifluoroethyl) Pyrazol-3-Yl]Pyridine-2-Carboxamide

All present enzymatic activity of Crystal Structure of Human Phosphodiesterase 10 in Complex with 6- Cyclopropyl-3-(Pyrimidin-5-Ylamino)-N-[1-(2,2,2-Trifluoroethyl) Pyrazol-3-Yl]Pyridine-2-Carboxamide:
3.1.4.17;

Protein crystallography data

The structure of Crystal Structure of Human Phosphodiesterase 10 in Complex with 6- Cyclopropyl-3-(Pyrimidin-5-Ylamino)-N-[1-(2,2,2-Trifluoroethyl) Pyrazol-3-Yl]Pyridine-2-Carboxamide, PDB code: 5sfk was solved by C.Joseph, R.M.Rodriguez-Sarmiento, 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) 43.48 / 2.33
Space group H 3
Cell size a, b, c (Å), α, β, γ (°) 135.55, 135.55, 233.95, 90, 90, 120
R / Rfree (%) 18.5 / 24.8

Other elements in 5sfk:

The structure of Crystal Structure of Human Phosphodiesterase 10 in Complex with 6- Cyclopropyl-3-(Pyrimidin-5-Ylamino)-N-[1-(2,2,2-Trifluoroethyl) Pyrazol-3-Yl]Pyridine-2-Carboxamide also contains other interesting chemical elements:

Fluorine (F) 12 atoms
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-3-(Pyrimidin-5-Ylamino)-N-[1-(2,2,2-Trifluoroethyl) Pyrazol-3-Yl]Pyridine-2-Carboxamide (pdb code 5sfk). 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-3-(Pyrimidin-5-Ylamino)-N-[1-(2,2,2-Trifluoroethyl) Pyrazol-3-Yl]Pyridine-2-Carboxamide, PDB code: 5sfk:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in 5sfk

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Zinc binding site 1 out of 4 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with 6- Cyclopropyl-3-(Pyrimidin-5-Ylamino)-N-[1-(2,2,2-Trifluoroethyl) Pyrazol-3-Yl]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-3-(Pyrimidin-5-Ylamino)-N-[1-(2,2,2-Trifluoroethyl) Pyrazol-3-Yl]Pyridine-2-Carboxamide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn801

b:39.1
occ:1.00
 NE2 A:HIS529 2.0 30.6 1.0
OD1 A:ASP674 2.1 41.2 1.0
NE2 A:HIS563 2.1 27.1 1.0
O A:HOH944 2.1 48.9 1.0
OD2 A:ASP564 2.2 32.8 1.0
CE1 A:HIS529 3.0 31.9 1.0
CG A:ASP674 3.0 35.0 1.0
CD2 A:HIS563 3.1 27.1 1.0
CD2 A:HIS529 3.1 31.4 1.0
CG A:ASP564 3.2 32.3 1.0
CE1 A:HIS563 3.2 28.0 1.0
O A:HOH906 3.2 43.8 1.0
OD2 A:ASP674 3.3 35.8 1.0
OD1 A:ASP564 3.7 32.7 1.0
MG A:MG802 3.8 41.5 1.0
CD2 A:HIS525 4.0 37.9 1.0
ND1 A:HIS529 4.1 31.1 1.0
O A:HOH955 4.1 38.3 1.0
CG A:HIS529 4.2 31.1 1.0
CG A:HIS563 4.2 26.9 1.0
ND1 A:HIS563 4.3 26.4 1.0
CB A:ASP564 4.3 29.2 1.0
CB A:ASP674 4.3 34.8 1.0
NE2 A:HIS525 4.5 33.4 1.0
O A:HOH988 4.6 48.1 1.0
CG2 A:VAL533 4.7 29.1 1.0
O A:HOH927 4.7 32.1 1.0
O A:ASP674 4.8 35.8 1.0
CA A:ASP674 4.8 29.7 1.0

Zinc binding site 2 out of 4 in 5sfk

Go back to Zinc Binding Sites List in 5sfk
Zinc binding site 2 out of 4 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with 6- Cyclopropyl-3-(Pyrimidin-5-Ylamino)-N-[1-(2,2,2-Trifluoroethyl) Pyrazol-3-Yl]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-3-(Pyrimidin-5-Ylamino)-N-[1-(2,2,2-Trifluoroethyl) Pyrazol-3-Yl]Pyridine-2-Carboxamide within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn801

b:36.1
occ:1.00
 OD2 B:ASP564 2.1 35.2 1.0
O B:HOH944 2.1 30.9 1.0
NE2 B:HIS529 2.1 26.5 1.0
OD1 B:ASP674 2.2 35.5 1.0
NE2 B:HIS563 2.2 30.3 1.0
CD2 B:HIS563 2.9 31.8 1.0
CD2 B:HIS529 3.0 28.1 1.0
CG B:ASP674 3.1 31.7 1.0
CE1 B:HIS529 3.1 27.7 1.0
CG B:ASP564 3.1 32.2 1.0
CE1 B:HIS563 3.3 32.4 1.0
OD2 B:ASP674 3.4 35.8 1.0
O B:HOH938 3.6 53.3 1.0
OD1 B:ASP564 3.7 31.7 1.0
MG B:MG802 3.9 41.0 1.0
CD2 B:HIS525 4.1 35.1 1.0
O B:HOH972 4.2 36.4 1.0
CG B:HIS563 4.2 31.7 1.0
CG B:HIS529 4.2 27.8 1.0
ND1 B:HIS529 4.2 30.9 1.0
O B:HOH987 4.2 52.5 1.0
CB B:ASP564 4.3 31.4 1.0
ND1 B:HIS563 4.3 32.6 1.0
CB B:ASP674 4.4 32.1 1.0
NE2 B:HIS525 4.5 34.6 1.0
O B:ASP674 4.6 36.0 1.0
CG2 B:VAL533 4.6 27.5 1.0
CA B:ASP674 4.8 33.5 1.0
O B:HOH966 4.9 26.6 1.0

Zinc binding site 3 out of 4 in 5sfk

Go back to Zinc Binding Sites List in 5sfk
Zinc binding site 3 out of 4 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with 6- Cyclopropyl-3-(Pyrimidin-5-Ylamino)-N-[1-(2,2,2-Trifluoroethyl) Pyrazol-3-Yl]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-3-(Pyrimidin-5-Ylamino)-N-[1-(2,2,2-Trifluoroethyl) Pyrazol-3-Yl]Pyridine-2-Carboxamide within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn801

b:36.4
occ:1.00
 O C:HOH909 1.8 24.2 1.0
NE2 C:HIS529 2.0 28.5 1.0
OD2 C:ASP564 2.0 32.4 1.0
OD1 C:ASP674 2.1 41.1 1.0
NE2 C:HIS563 2.2 28.1 1.0
CD2 C:HIS529 2.9 29.2 1.0
CG C:ASP674 3.0 34.2 1.0
CE1 C:HIS529 3.0 30.3 1.0
CD2 C:HIS563 3.1 25.7 1.0
CE1 C:HIS563 3.2 27.4 1.0
CG C:ASP564 3.2 34.5 1.0
OD2 C:ASP674 3.2 36.5 1.0
MG C:MG802 3.8 39.9 1.0
OD1 C:ASP564 3.8 33.5 1.0
CD2 C:HIS525 4.0 37.6 1.0
CG C:HIS529 4.1 29.9 1.0
O C:HOH942 4.1 46.8 1.0
ND1 C:HIS529 4.1 30.3 1.0
ND1 C:HIS563 4.2 24.5 1.0
CB C:ASP564 4.3 31.8 1.0
CG C:HIS563 4.3 25.0 1.0
CB C:ASP674 4.4 35.0 1.0
NE2 C:HIS525 4.5 39.4 1.0
O C:HOH990 4.7 43.5 1.0
CG2 C:VAL533 4.7 28.1 1.0
O C:ASP674 4.8 36.7 1.0
CA C:ASP674 4.8 33.3 1.0
O C:HOH947 4.8 34.4 1.0

Zinc binding site 4 out of 4 in 5sfk

Go back to Zinc Binding Sites List in 5sfk
Zinc binding site 4 out of 4 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with 6- Cyclopropyl-3-(Pyrimidin-5-Ylamino)-N-[1-(2,2,2-Trifluoroethyl) Pyrazol-3-Yl]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-3-(Pyrimidin-5-Ylamino)-N-[1-(2,2,2-Trifluoroethyl) Pyrazol-3-Yl]Pyridine-2-Carboxamide within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn801

b:60.4
occ:1.00
 NE2 D:HIS563 2.1 44.2 1.0
O D:HOH917 2.2 49.6 1.0
NE2 D:HIS529 2.3 56.2 1.0
O D:HOH909 2.3 31.5 1.0
OD1 D:ASP674 2.3 73.6 1.0
OD2 D:ASP564 2.5 61.2 1.0
CD2 D:HIS563 3.0 46.9 1.0
CE1 D:HIS563 3.1 47.4 1.0
CD2 D:HIS529 3.2 57.4 1.0
CG D:ASP564 3.3 52.0 1.0
CE1 D:HIS529 3.3 60.6 1.0
CG D:ASP674 3.3 68.7 1.0
OD2 D:ASP674 3.9 72.3 1.0
OD1 D:ASP564 3.9 52.4 1.0
CB D:ASP564 4.1 52.5 1.0
CG D:HIS563 4.2 53.7 1.0
ND1 D:HIS563 4.2 47.7 1.0
MG D:MG802 4.2 69.3 1.0
CD2 D:HIS525 4.2 52.3 1.0
CG D:HIS529 4.4 53.4 1.0
ND1 D:HIS529 4.4 62.0 1.0
O D:HOH922 4.4 56.6 1.0
CB D:ASP674 4.5 70.6 1.0
CG2 D:VAL533 4.7 56.3 1.0
O D:ASP674 4.7 72.8 1.0
NE2 D:HIS525 4.8 53.0 1.0
CA D:ASP674 4.9 69.3 1.0
O D:HOH910 4.9 51.5 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 04:58:09 2024

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