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Zinc in PDB 5sdy: Crystal Structure of Human Phosphodiesterase 10 in Complex with 6- Cyclopropyl-N-[5-(Dimethylcarbamoyl)-1-(2-Methoxyethyl)Pyrazol-4-Yl]- 3-(Pyrimidin-5-Ylamino)Pyridine-2-Carboxamide

Enzymatic activity of Crystal Structure of Human Phosphodiesterase 10 in Complex with 6- Cyclopropyl-N-[5-(Dimethylcarbamoyl)-1-(2-Methoxyethyl)Pyrazol-4-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-[5-(Dimethylcarbamoyl)-1-(2-Methoxyethyl)Pyrazol-4-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-[5-(Dimethylcarbamoyl)-1-(2-Methoxyethyl)Pyrazol-4-Yl]- 3-(Pyrimidin-5-Ylamino)Pyridine-2-Carboxamide, PDB code: 5sdy 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)*	44.76 / 2.20
*Space group*	I 2 3
*Cell size a, b, c (Å), α, β, γ (°)*	141.546, 141.546, 141.546, 90, 90, 90
*R / R_free (%)*	18.1 / 22.3

Other elements in 5sdy:

Magnesium

(Mg)

1 atom

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of Human Phosphodiesterase 10 in Complex with 6- Cyclopropyl-N-[5-(Dimethylcarbamoyl)-1-(2-Methoxyethyl)Pyrazol-4-Yl]- 3-(Pyrimidin-5-Ylamino)Pyridine-2-Carboxamide (pdb code 5sdy). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total only one binding site of Zinc was determined in the Crystal Structure of Human Phosphodiesterase 10 in Complex with 6- Cyclopropyl-N-[5-(Dimethylcarbamoyl)-1-(2-Methoxyethyl)Pyrazol-4-Yl]- 3-(Pyrimidin-5-Ylamino)Pyridine-2-Carboxamide, PDB code: 5sdy:

Zinc binding site 1 out of 1 in 5sdy

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Zinc Binding Sites List in 5sdy

Zinc binding site 1 out of 1 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with 6- Cyclopropyl-N-[5-(Dimethylcarbamoyl)-1-(2-Methoxyethyl)Pyrazol-4-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-[5-(Dimethylcarbamoyl)-1-(2-Methoxyethyl)Pyrazol-4-Yl]- 3-(Pyrimidin-5-Ylamino)Pyridine-2-Carboxamide within 5.0Å range:

probe	atom	residue	distance (Å)	B	Occ
A:Zn801 b:35.4 occ:1.00	O	A:HOH996	2.0	26.6	1.0
	NE2	A:HIS529	2.1	27.4	1.0
	OD1	A:ASP674	2.1	32.0	1.0
	NE2	A:HIS563	2.1	28.8	1.0
	OD2	A:ASP564	2.2	30.2	1.0
	O	A:HOH938	2.9	45.5	1.0
	CD2	A:HIS563	3.0	26.4	1.0
	CD2	A:HIS529	3.1	27.7	1.0
	CE1	A:HIS529	3.1	28.2	1.0
	CG	A:ASP674	3.1	28.5	1.0
	CE1	A:HIS563	3.2	27.7	1.0
	CG	A:ASP564	3.2	29.6	1.0
	OD2	A:ASP674	3.4	32.6	1.0
	OD1	A:ASP564	3.7	29.4	1.0
	MG	A:MG802	3.8	24.8	1.0
	CD2	A:HIS525	4.1	33.9	1.0
	O	A:HOH1007	4.1	43.7	1.0
	O	A:HOH1052	4.2	31.4	1.0
	ND1	A:HIS529	4.2	28.2	1.0
	CG	A:HIS529	4.2	28.2	1.0
	CG	A:HIS563	4.2	26.9	1.0
	ND1	A:HIS563	4.2	27.4	1.0
	CB	A:ASP564	4.3	28.2	1.0
	CB	A:ASP674	4.4	28.5	1.0
	NE2	A:HIS525	4.5	37.1	1.0
	CG2	A:VAL533	4.6	27.6	1.0
	O	A:HOH944	4.7	29.0	1.0
	O	A:ASP674	4.7	27.8	1.0
	CA	A:ASP674	4.8	28.5	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: Thu Aug 21 07:31:36 2025

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