Zinc in PDB 5sfu: Crystal Structure of Human Phosphodiesterase 10 in Complex with 6- Cyclopropyl-3-(Pyrimidin-5-Ylamino)-N-[4-(Pyrrolidine-1-Carbonyl) Pyridin-3-Yl]Pyridine-2-Carboxamide

Enzymatic activity of Crystal Structure of Human Phosphodiesterase 10 in Complex with 6- Cyclopropyl-3-(Pyrimidin-5-Ylamino)-N-[4-(Pyrrolidine-1-Carbonyl) Pyridin-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-[4-(Pyrrolidine-1-Carbonyl) Pyridin-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-[4-(Pyrrolidine-1-Carbonyl) Pyridin-3-Yl]Pyridine-2-Carboxamide, PDB code: 5sfu 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) 43.55 / 2.40
Space group H 3
Cell size a, b, c (Å), α, β, γ (°) 135.029, 135.029, 234.652, 90, 90, 120
R / Rfree (%) 19.2 / 25.6

Other elements in 5sfu:

The structure of Crystal Structure of Human Phosphodiesterase 10 in Complex with 6- Cyclopropyl-3-(Pyrimidin-5-Ylamino)-N-[4-(Pyrrolidine-1-Carbonyl) Pyridin-3-Yl]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-3-(Pyrimidin-5-Ylamino)-N-[4-(Pyrrolidine-1-Carbonyl) Pyridin-3-Yl]Pyridine-2-Carboxamide (pdb code 5sfu). 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-[4-(Pyrrolidine-1-Carbonyl) Pyridin-3-Yl]Pyridine-2-Carboxamide, PDB code: 5sfu:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in 5sfu

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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-[4-(Pyrrolidine-1-Carbonyl) Pyridin-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-[4-(Pyrrolidine-1-Carbonyl) Pyridin-3-Yl]Pyridine-2-Carboxamide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn801

b:41.2
occ:1.00
 NE2 A:HIS563 2.1 30.1 1.0
O A:HOH924 2.1 29.9 1.0
OD2 A:ASP564 2.1 35.6 1.0
OD1 A:ASP674 2.1 48.8 1.0
NE2 A:HIS529 2.1 35.3 1.0
O A:HOH948 2.6 42.4 1.0
CD2 A:HIS563 3.0 31.8 1.0
CG A:ASP674 3.0 38.5 1.0
CE1 A:HIS563 3.1 30.6 1.0
CD2 A:HIS529 3.1 34.5 1.0
CE1 A:HIS529 3.1 35.9 1.0
CG A:ASP564 3.2 33.0 1.0
OD2 A:ASP674 3.3 42.5 1.0
OD1 A:ASP564 3.8 36.4 1.0
MG A:MG802 3.8 31.1 1.0
O A:HOH918 4.1 46.7 1.0
CG A:HIS563 4.1 30.6 1.0
ND1 A:HIS563 4.1 30.1 1.0
ND1 A:HIS529 4.2 34.9 1.0
CD2 A:HIS525 4.2 35.1 1.0
CG A:HIS529 4.2 32.0 1.0
O A:HOH959 4.3 32.1 1.0
CB A:ASP564 4.3 31.3 1.0
CB A:ASP674 4.4 40.0 1.0
O A:HOH906 4.5 31.6 1.0
CG2 A:VAL533 4.6 30.2 1.0
NE2 A:HIS525 4.6 33.3 1.0
O A:ASP674 4.7 40.8 1.0
CA A:ASP674 4.8 35.5 1.0

Zinc binding site 2 out of 4 in 5sfu

Go back to Zinc Binding Sites List in 5sfu
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-[4-(Pyrrolidine-1-Carbonyl) Pyridin-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-[4-(Pyrrolidine-1-Carbonyl) Pyridin-3-Yl]Pyridine-2-Carboxamide within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn801

b:37.5
occ:1.00
 NE2 B:HIS563 2.1 31.0 1.0
OD2 B:ASP564 2.1 32.7 1.0
OD1 B:ASP674 2.1 40.5 1.0
NE2 B:HIS529 2.2 33.8 1.0
O B:HOH919 2.3 19.4 1.0
CG B:ASP674 3.0 35.4 1.0
CD2 B:HIS563 3.1 32.4 1.0
CD2 B:HIS529 3.1 32.5 1.0
CG B:ASP564 3.1 32.4 1.0
CE1 B:HIS563 3.1 33.8 1.0
OD2 B:ASP674 3.2 38.9 1.0
CE1 B:HIS529 3.2 36.0 1.0
OD1 B:ASP564 3.6 33.8 1.0
MG B:MG802 3.9 28.5 1.0
O B:HOH940 3.9 31.2 1.0
CD2 B:HIS525 4.1 38.7 1.0
CG B:HIS563 4.2 31.4 1.0
ND1 B:HIS563 4.2 31.2 1.0
CG B:HIS529 4.3 34.1 1.0
CB B:ASP564 4.3 32.5 1.0
ND1 B:HIS529 4.3 33.0 1.0
O B:HOH943 4.3 46.2 1.0
CB B:ASP674 4.3 35.5 1.0
NE2 B:HIS525 4.5 36.2 1.0
O B:HOH915 4.6 30.6 1.0
O B:ASP674 4.7 37.5 1.0
CA B:ASP674 4.8 33.7 1.0
CG2 B:VAL533 4.9 30.6 1.0

Zinc binding site 3 out of 4 in 5sfu

Go back to Zinc Binding Sites List in 5sfu
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-[4-(Pyrrolidine-1-Carbonyl) Pyridin-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-[4-(Pyrrolidine-1-Carbonyl) Pyridin-3-Yl]Pyridine-2-Carboxamide within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn801

b:39.1
occ:1.00
 OD2 C:ASP564 2.0 41.6 1.0
NE2 C:HIS529 2.1 35.6 1.0
O C:HOH915 2.1 26.4 1.0
NE2 C:HIS563 2.1 31.5 1.0
OD1 C:ASP674 2.2 38.9 1.0
CE1 C:HIS529 3.0 30.9 1.0
CG C:ASP674 3.0 35.2 1.0
CG C:ASP564 3.1 32.9 1.0
CD2 C:HIS529 3.1 33.8 1.0
CE1 C:HIS563 3.1 32.2 1.0
CD2 C:HIS563 3.2 30.9 1.0
OD2 C:ASP674 3.2 34.1 1.0
OD1 C:ASP564 3.6 37.0 1.0
MG C:MG802 3.9 31.8 1.0
CD2 C:HIS525 4.1 45.2 1.0
ND1 C:HIS529 4.1 30.0 1.0
CG C:HIS529 4.2 30.3 1.0
ND1 C:HIS563 4.2 26.6 1.0
CB C:ASP564 4.2 32.2 1.0
CG C:HIS563 4.3 30.5 1.0
O C:HOH936 4.4 45.3 1.0
O C:HOH964 4.4 32.3 1.0
CB C:ASP674 4.4 36.7 1.0
NE2 C:HIS525 4.5 43.6 1.0
O C:HOH934 4.5 33.4 1.0
O C:ASP674 4.8 33.6 1.0
CA C:ASP674 4.8 36.3 1.0
CG2 C:VAL533 4.8 33.2 1.0

Zinc binding site 4 out of 4 in 5sfu

Go back to Zinc Binding Sites List in 5sfu
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-[4-(Pyrrolidine-1-Carbonyl) Pyridin-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-[4-(Pyrrolidine-1-Carbonyl) Pyridin-3-Yl]Pyridine-2-Carboxamide within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn801

b:66.1
occ:1.00
 NE2 D:HIS563 2.1 49.1 1.0
NE2 D:HIS529 2.2 62.8 1.0
O D:HOH913 2.2 64.0 1.0
OD1 D:ASP674 2.3 58.1 1.0
OD2 D:ASP564 2.3 65.7 1.0
O D:HOH915 2.4 37.3 1.0
CD2 D:HIS563 3.0 50.9 1.0
CD2 D:HIS529 3.1 65.2 1.0
CE1 D:HIS563 3.2 51.5 1.0
CE1 D:HIS529 3.3 64.8 1.0
CG D:ASP564 3.3 57.9 1.0
CG D:ASP674 3.4 59.2 1.0
OD1 D:ASP564 3.9 56.4 1.0
O D:HOH911 4.0 48.3 1.0
OD2 D:ASP674 4.0 67.0 1.0
MG D:MG802 4.1 52.6 1.0
CD2 D:HIS525 4.2 70.2 1.0
CG D:HIS563 4.2 52.1 1.0
CB D:ASP564 4.2 59.8 1.0
ND1 D:HIS563 4.3 53.7 1.0
CG D:HIS529 4.3 62.9 1.0
ND1 D:HIS529 4.3 66.2 1.0
O D:HOH903 4.5 47.1 1.0
CB D:ASP674 4.5 61.6 1.0
O D:ASP674 4.6 69.6 1.0
NE2 D:HIS525 4.7 70.4 1.0
CG2 D:VAL533 4.7 60.3 1.0
CA D:ASP674 4.8 61.3 1.0
O D:HOH912 4.9 41.7 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 05:04:36 2024

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