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Zinc in PDB 5sfl: Crystal Structure of Human Phosphodiesterase 10 in Complex with 6- Cyclopropyl-N-[5-[(2-Hydroxy-2-Methylpropyl)Carbamoyl]-1- Methylpyrazol-4-Yl]-3-(Pyrimidin-5-Ylamino)Pyrazine-2-Carboxamide

Enzymatic activity of Crystal Structure of Human Phosphodiesterase 10 in Complex with 6- Cyclopropyl-N-[5-[(2-Hydroxy-2-Methylpropyl)Carbamoyl]-1- Methylpyrazol-4-Yl]-3-(Pyrimidin-5-Ylamino)Pyrazine-2-Carboxamide

All present enzymatic activity of Crystal Structure of Human Phosphodiesterase 10 in Complex with 6- Cyclopropyl-N-[5-[(2-Hydroxy-2-Methylpropyl)Carbamoyl]-1- Methylpyrazol-4-Yl]-3-(Pyrimidin-5-Ylamino)Pyrazine-2-Carboxamide:
3.1.4.17;

Protein crystallography data

The structure of Crystal Structure of Human Phosphodiesterase 10 in Complex with 6- Cyclopropyl-N-[5-[(2-Hydroxy-2-Methylpropyl)Carbamoyl]-1- Methylpyrazol-4-Yl]-3-(Pyrimidin-5-Ylamino)Pyrazine-2-Carboxamide, PDB code: 5sfl 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) 43.44 / 2.13
Space group H 3
Cell size a, b, c (Å), α, β, γ (°) 135.036, 135.036, 234.927, 90, 90, 120
R / Rfree (%) 18.7 / 22.7

Other elements in 5sfl:

The structure of Crystal Structure of Human Phosphodiesterase 10 in Complex with 6- Cyclopropyl-N-[5-[(2-Hydroxy-2-Methylpropyl)Carbamoyl]-1- Methylpyrazol-4-Yl]-3-(Pyrimidin-5-Ylamino)Pyrazine-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-[5-[(2-Hydroxy-2-Methylpropyl)Carbamoyl]-1- Methylpyrazol-4-Yl]-3-(Pyrimidin-5-Ylamino)Pyrazine-2-Carboxamide (pdb code 5sfl). 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-[5-[(2-Hydroxy-2-Methylpropyl)Carbamoyl]-1- Methylpyrazol-4-Yl]-3-(Pyrimidin-5-Ylamino)Pyrazine-2-Carboxamide, PDB code: 5sfl:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in 5sfl

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

b:37.5
occ:1.00
 OD2 A:ASP564 2.0 35.2 1.0
NE2 A:HIS563 2.1 33.4 1.0
NE2 A:HIS529 2.1 34.0 1.0
OD1 A:ASP674 2.2 33.8 1.0
O A:HOH965 2.2 31.1 1.0
O A:HOH976 2.6 49.5 1.0
CD2 A:HIS563 2.9 31.4 1.0
CG A:ASP674 3.1 33.9 1.0
CG A:ASP564 3.1 32.1 1.0
CD2 A:HIS529 3.1 31.8 1.0
CE1 A:HIS529 3.1 33.2 1.0
CE1 A:HIS563 3.2 33.9 1.0
OD2 A:ASP674 3.3 38.4 1.0
OD1 A:ASP564 3.6 31.9 1.0
MG A:MG802 3.7 31.8 1.0
CG A:HIS563 4.1 31.8 1.0
O A:HOH989 4.1 28.9 1.0
O A:HOH961 4.2 38.4 1.0
CD2 A:HIS525 4.2 36.9 1.0
ND1 A:HIS563 4.2 31.9 1.0
ND1 A:HIS529 4.2 32.0 1.0
CG A:HIS529 4.2 32.3 1.0
CB A:ASP564 4.3 31.3 1.0
CB A:ASP674 4.4 32.6 1.0
NE2 A:HIS525 4.5 36.6 1.0
O A:HOH941 4.6 28.1 1.0
CG2 A:VAL533 4.7 29.0 1.0
O A:ASP674 4.8 31.4 1.0
CA A:ASP674 4.8 30.3 1.0

Zinc binding site 2 out of 4 in 5sfl

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

b:35.8
occ:1.00
 O B:HOH952 2.1 28.9 1.0
NE2 B:HIS563 2.1 28.3 1.0
OD2 B:ASP564 2.1 32.6 1.0
NE2 B:HIS529 2.1 30.2 1.0
OD1 B:ASP674 2.2 32.2 1.0
O B:HOH944 2.5 47.6 1.0
CD2 B:HIS563 3.0 28.7 1.0
CG B:ASP674 3.1 32.2 1.0
CD2 B:HIS529 3.1 29.2 1.0
CG B:ASP564 3.1 28.8 1.0
CE1 B:HIS563 3.1 29.7 1.0
CE1 B:HIS529 3.2 30.6 1.0
OD2 B:ASP674 3.3 32.1 1.0
OD1 B:ASP564 3.6 29.8 1.0
MG B:MG802 3.7 29.5 1.0
O B:HOH959 4.0 36.4 1.0
O B:HOH1000 4.1 27.1 1.0
CD2 B:HIS525 4.1 30.9 1.0
CG B:HIS563 4.2 30.1 1.0
ND1 B:HIS563 4.2 31.2 1.0
CG B:HIS529 4.2 30.2 1.0
ND1 B:HIS529 4.3 30.7 1.0
CB B:ASP564 4.3 28.6 1.0
NE2 B:HIS525 4.4 32.8 1.0
CB B:ASP674 4.5 30.5 1.0
O B:HOH932 4.5 28.6 1.0
O B:HOH1002 4.7 53.5 1.0
CG2 B:VAL533 4.7 31.7 1.0
O B:ASP674 4.8 31.8 1.0
CA B:ASP674 4.9 29.5 1.0

Zinc binding site 3 out of 4 in 5sfl

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

b:39.2
occ:1.00
 O C:HOH943 2.1 31.3 1.0
NE2 C:HIS563 2.1 33.5 1.0
OD2 C:ASP564 2.1 32.0 1.0
NE2 C:HIS529 2.1 32.4 1.0
OD1 C:ASP674 2.2 35.7 1.0
CD2 C:HIS563 3.0 31.3 1.0
CG C:ASP674 3.1 34.9 1.0
CD2 C:HIS529 3.1 33.2 1.0
CG C:ASP564 3.1 31.4 1.0
CE1 C:HIS529 3.1 36.9 1.0
CE1 C:HIS563 3.2 31.5 1.0
OD2 C:ASP674 3.3 34.9 1.0
OD1 C:ASP564 3.6 31.8 1.0
MG C:MG802 3.7 32.0 1.0
CD2 C:HIS525 4.1 37.9 1.0
CG C:HIS563 4.2 32.1 1.0
O C:HOH979 4.2 28.5 1.0
O C:HOH965 4.2 40.4 1.0
ND1 C:HIS529 4.2 36.4 1.0
ND1 C:HIS563 4.2 30.4 1.0
CG C:HIS529 4.2 35.6 1.0
CB C:ASP564 4.3 30.2 1.0
CB C:ASP674 4.4 36.2 1.0
NE2 C:HIS525 4.5 36.3 1.0
O C:HOH933 4.5 32.7 1.0
CG2 C:VAL533 4.7 31.3 1.0
O C:ASP674 4.8 38.6 1.0
CA C:ASP674 4.8 37.0 1.0

Zinc binding site 4 out of 4 in 5sfl

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

b:47.0
occ:1.00
 NE2 D:HIS563 2.1 36.3 1.0
O D:HOH910 2.1 29.4 1.0
NE2 D:HIS529 2.1 44.7 1.0
OD2 D:ASP564 2.2 44.4 1.0
OD1 D:ASP674 2.2 39.2 1.0
O D:HOH950 2.4 45.5 1.0
CD2 D:HIS563 2.9 36.1 1.0
CG D:ASP674 3.1 40.0 1.0
CG D:ASP564 3.1 38.8 1.0
CD2 D:HIS529 3.1 42.8 1.0
CE1 D:HIS529 3.1 41.2 1.0
CE1 D:HIS563 3.2 39.1 1.0
OD2 D:ASP674 3.2 41.2 1.0
OD1 D:ASP564 3.6 38.6 1.0
MG D:MG802 3.8 40.8 1.0
O D:HOH914 4.0 42.0 1.0
CG D:HIS563 4.1 34.1 1.0
O D:HOH958 4.1 42.4 1.0
CB D:ASP564 4.2 37.1 1.0
CD2 D:HIS525 4.2 47.5 1.0
ND1 D:HIS563 4.2 35.6 1.0
ND1 D:HIS529 4.2 42.3 1.0
CG D:HIS529 4.2 40.8 1.0
O D:HOH920 4.4 38.3 1.0
CB D:ASP674 4.4 40.1 1.0
NE2 D:HIS525 4.6 48.0 1.0
O D:ASP674 4.7 40.0 1.0
CG2 D:VAL533 4.8 43.7 1.0
CA D:ASP674 4.8 40.5 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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