Magnesium in PDB 5set: Crystal Structure of Human Phosphodiesterase 10 in Complex with 6- Cyclopropyl-N-(2-Methyl-5-Pyridin-2-Ylpyrazol-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-Methyl-5-Pyridin-2-Ylpyrazol-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-Methyl-5-Pyridin-2-Ylpyrazol-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-Methyl-5-Pyridin-2-Ylpyrazol-3-Yl)-3-(Pyrimidin-5- Ylamino)Pyridine-2-Carboxamide, PDB code: 5set 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)*	37.84 / 2.40
*Space group*	I 2 3
*Cell size a, b, c (Å), α, β, γ (°)*	141.484, 141.484, 141.484, 90, 90, 90
*R / R_free (%)*	18.2 / 22.9

Other elements in 5set:

Zinc

(Zn)

1 atom

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of Human Phosphodiesterase 10 in Complex with 6- Cyclopropyl-N-(2-Methyl-5-Pyridin-2-Ylpyrazol-3-Yl)-3-(Pyrimidin-5- Ylamino)Pyridine-2-Carboxamide (pdb code 5set). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total only one binding site of Magnesium was determined in the Crystal Structure of Human Phosphodiesterase 10 in Complex with 6- Cyclopropyl-N-(2-Methyl-5-Pyridin-2-Ylpyrazol-3-Yl)-3-(Pyrimidin-5- Ylamino)Pyridine-2-Carboxamide, PDB code: 5set:

Magnesium binding site 1 out of 1 in 5set

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Magnesium Binding Sites List in 5set

Magnesium binding site 1 out of 1 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with 6- Cyclopropyl-N-(2-Methyl-5-Pyridin-2-Ylpyrazol-3-Yl)-3-(Pyrimidin-5- Ylamino)Pyridine-2-Carboxamide

Mono view

Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Crystal Structure of Human Phosphodiesterase 10 in Complex with 6- Cyclopropyl-N-(2-Methyl-5-Pyridin-2-Ylpyrazol-3-Yl)-3-(Pyrimidin-5- Ylamino)Pyridine-2-Carboxamide within 5.0Å range:

probe	atom	residue	distance (Å)	B	Occ
A:Mg802 b:37.2 occ:1.00	O	A:HOH926	1.8	42.9	1.0
	O	A:HOH922	1.9	38.6	1.0
	O	A:HOH905	1.9	42.4	1.0
	OD1	A:ASP564	2.0	44.1	1.0
	O	A:HOH919	2.0	37.9	1.0
	O	A:HOH932	2.3	52.9	1.0
	CG	A:ASP564	3.0	41.7	1.0
	OD2	A:ASP564	3.4	43.2	1.0
	ZN	A:ZN801	3.8	51.1	1.0
	NE2	A:HIS595	3.9	50.3	1.0
	OE2	A:GLU592	4.0	54.5	1.0
	O	A:HOH911	4.1	52.3	1.0
	CD2	A:HIS563	4.2	44.8	1.0
	OG1	A:THR633	4.2	44.5	1.0
	CD2	A:HIS567	4.2	48.4	1.0
	O	A:HIS563	4.3	46.6	1.0
	CB	A:ASP564	4.3	44.3	1.0
	CD2	A:HIS595	4.4	53.8	1.0
	NE2	A:HIS567	4.5	51.8	1.0
	OD2	A:ASP674	4.6	43.5	1.0
	O	A:THR633	4.6	48.9	1.0
	NE2	A:HIS563	4.6	39.6	1.0
	CD2	A:HIS525	4.7	50.0	1.0
	CA	A:ASP564	4.7	43.6	1.0
	CB	A:THR633	4.8	53.2	1.0
	NE2	A:HIS525	4.8	54.6	1.0
	CD	A:GLU592	4.9	55.0	1.0
	CE1	A:HIS595	5.0	56.0	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: Tue Aug 12 19:23:23 2025

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