Atomistry » Zinc » PDB 5rmm-5ser » 5sea
Atomistry »
  Zinc »
    PDB 5rmm-5ser »
      5sea »

Zinc in PDB 5sea: Crystal Structure of Human Phosphodiesterase 10 in Complex with 6- Cyclopropyl-N-(2-Phenylpyrazol-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-Phenylpyrazol-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-Phenylpyrazol-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-Phenylpyrazol-3-Yl)-3-(Pyrimidin-5-Ylamino)Pyridine- 2-Carboxamide, PDB code: 5sea 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) 41.66 / 2.00
Space group H 3
Cell size a, b, c (Å), α, β, γ (°) 136.069, 136.069, 235.628, 90, 90, 120
R / Rfree (%) 19.5 / 22.8

Other elements in 5sea:

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

Zinc binding site 1 out of 4 in 5sea

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

b:28.0
occ:1.00
 OD2 A:ASP564 2.1 22.7 1.0
NE2 A:HIS563 2.2 24.1 1.0
NE2 A:HIS529 2.2 24.7 1.0
O A:HOH961 2.2 35.1 1.0
OD1 A:ASP674 2.2 26.4 1.0
O A:HOH951 2.2 21.5 1.0
CD2 A:HIS563 2.9 22.2 1.0
CG A:ASP674 3.1 27.4 1.0
CG A:ASP564 3.1 23.8 1.0
CD2 A:HIS529 3.1 24.0 1.0
CE1 A:HIS529 3.2 24.5 1.0
CE1 A:HIS563 3.3 26.1 1.0
OD2 A:ASP674 3.3 30.5 1.0
OD1 A:ASP564 3.6 22.4 1.0
MG A:MG802 3.8 23.8 1.0
CG A:HIS563 4.1 23.1 1.0
CD2 A:HIS525 4.2 26.9 1.0
CG A:HIS529 4.2 24.1 1.0
CB A:ASP564 4.2 24.5 1.0
ND1 A:HIS563 4.3 24.7 1.0
O A:HOH974 4.3 30.5 1.0
ND1 A:HIS529 4.3 22.9 1.0
O A:HOH1004 4.3 22.0 1.0
CB A:ASP674 4.4 26.1 1.0
O A:HOH920 4.5 22.4 1.0
NE2 A:HIS525 4.6 26.5 1.0
O A:HOH1024 4.6 56.0 1.0
CG2 A:VAL533 4.7 22.8 1.0
O A:ASP674 4.8 26.1 1.0
CA A:ASP674 4.8 24.4 1.0

Zinc binding site 2 out of 4 in 5sea

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

b:27.0
occ:1.00
 O B:HOH965 2.1 18.5 1.0
OD2 B:ASP564 2.1 21.3 1.0
NE2 B:HIS563 2.2 19.9 1.0
OD1 B:ASP674 2.2 23.2 1.0
NE2 B:HIS529 2.2 20.2 1.0
O B:HOH963 2.5 37.0 1.0
CD2 B:HIS563 3.0 19.7 1.0
CG B:ASP674 3.0 23.9 1.0
CG B:ASP564 3.1 21.8 1.0
CD2 B:HIS529 3.1 21.8 1.0
CE1 B:HIS529 3.2 21.2 1.0
CE1 B:HIS563 3.2 21.1 1.0
OD2 B:ASP674 3.3 25.8 1.0
OD1 B:ASP564 3.6 20.2 1.0
MG B:MG802 3.7 22.0 1.0
O B:HOH1028 4.0 20.8 1.0
CD2 B:HIS525 4.1 25.3 1.0
O B:HOH979 4.1 23.9 1.0
CG B:HIS563 4.2 19.8 1.0
ND1 B:HIS563 4.3 20.7 1.0
CB B:ASP564 4.3 22.2 1.0
CG B:HIS529 4.3 21.6 1.0
ND1 B:HIS529 4.3 20.8 1.0
CB B:ASP674 4.4 23.6 1.0
NE2 B:HIS525 4.4 25.7 1.0
O B:HOH950 4.6 19.5 1.0
O B:HOH1046 4.7 51.7 1.0
CG2 B:VAL533 4.7 21.4 1.0
O B:ASP674 4.8 21.6 1.0
CA B:ASP674 4.9 22.5 1.0

Zinc binding site 3 out of 4 in 5sea

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

b:28.6
occ:1.00
 O C:HOH949 2.0 20.5 1.0
OD2 C:ASP564 2.1 23.4 1.0
NE2 C:HIS529 2.1 24.5 1.0
NE2 C:HIS563 2.1 25.2 1.0
OD1 C:ASP674 2.2 24.1 1.0
O C:HOH1009 2.4 36.8 1.0
CD2 C:HIS563 3.0 24.4 1.0
CG C:ASP674 3.1 27.3 1.0
CD2 C:HIS529 3.1 22.4 1.0
CG C:ASP564 3.1 23.2 1.0
CE1 C:HIS529 3.1 24.2 1.0
CE1 C:HIS563 3.2 24.6 1.0
OD2 C:ASP674 3.4 32.9 1.0
OD1 C:ASP564 3.6 23.2 1.0
MG C:MG802 3.8 24.2 1.0
CD2 C:HIS525 4.1 27.0 1.0
O C:HOH1037 4.1 22.0 1.0
CG C:HIS563 4.2 25.5 1.0
O C:HOH984 4.2 32.9 1.0
ND1 C:HIS529 4.2 23.6 1.0
ND1 C:HIS563 4.2 24.5 1.0
CG C:HIS529 4.2 23.3 1.0
CB C:ASP564 4.3 22.6 1.0
CB C:ASP674 4.4 25.6 1.0
NE2 C:HIS525 4.5 28.8 1.0
O C:HOH941 4.7 24.4 1.0
O C:HOH1047 4.7 54.7 1.0
CA C:ASP674 4.8 25.0 1.0
CG2 C:VAL533 4.8 23.5 1.0
O C:ASP674 4.8 25.6 1.0

Zinc binding site 4 out of 4 in 5sea

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

b:32.4
occ:1.00
 O D:HOH928 2.0 24.0 1.0
NE2 D:HIS563 2.1 22.3 1.0
OD2 D:ASP564 2.2 28.6 1.0
NE2 D:HIS529 2.2 28.9 1.0
OD1 D:ASP674 2.2 26.1 1.0
O D:HOH980 2.4 40.6 1.0
CD2 D:HIS563 3.0 24.9 1.0
CD2 D:HIS529 3.1 29.9 1.0
CG D:ASP564 3.1 25.6 1.0
CG D:ASP674 3.1 27.5 1.0
CE1 D:HIS563 3.2 24.5 1.0
CE1 D:HIS529 3.2 30.0 1.0
OD2 D:ASP674 3.4 29.6 1.0
OD1 D:ASP564 3.6 26.6 1.0
MG D:MG802 3.8 31.8 1.0
O D:HOH988 4.1 25.7 1.0
O D:HOH927 4.1 35.1 1.0
CD2 D:HIS525 4.2 34.8 1.0
CG D:HIS563 4.2 25.0 1.0
ND1 D:HIS563 4.3 23.9 1.0
CB D:ASP564 4.3 26.0 1.0
CG D:HIS529 4.3 28.3 1.0
ND1 D:HIS529 4.3 28.8 1.0
CB D:ASP674 4.5 27.9 1.0
O D:HOH914 4.6 27.1 1.0
NE2 D:HIS525 4.7 34.6 1.0
CG2 D:VAL533 4.8 27.6 1.0
O D:ASP674 4.8 29.8 1.0
CA D:ASP674 4.8 28.2 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 04:38:43 2024

Last articles

Zn in 9MJ5
Zn in 9HNW
Zn in 9G0L
Zn in 9FNE
Zn in 9DZN
Zn in 9E0I
Zn in 9D32
Zn in 9DAK
Zn in 8ZXC
Zn in 8ZUF
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy