scPDB - 2dgn entry

Protein Data Bank Entry:

PDB ID : 2dgn

Resolution :2.400 Å

Experimental Method : X-ray

Deposition Date : 2006-03-15

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Adenylosuccinate synthetase isozyme 1
ID:	PURA1_MOUSE
AC:	P28650
Organism:	Mus musculus
Reign:	Eukaryota
TaxID:	10090
EC Number:	/

Chains:

Chain Name:	Percentage of Residues within binding site
A	100 %

Ligand binding site composition:

B-Factor:	27.175
Number of residues:	44
Including
Standard Amino Acids:	37
Non Standard Amino Acids:	2
Water Molecules:	5
Cofactors:	GDP
Metals:	MG

Cavity properties

Ligandability	Volume (Å3)
0.886	705.375

% Hydrophobic	% Polar
36.36	63.64
According to VolSite

Ligand :

HET Code:	DOI
Formula:	C10H10N4O10P2
Molecular weight:	408.155 g/mol
DrugBank ID:	-
Buried Surface Area:	78.65 %
Polar Surface area:	237.52 Å2

Number of
H-Bond Acceptors:	13
H-Bond Donors:	1
Rings:	3
Aromatic rings:	2
Anionic atoms:	4
Cationic atoms:	0
Rule of Five Violation:	1
Rotatable Bonds:	6

Mass center Coordinates

X	Y	Z
62.3419	62.9042	37.5419

Binding mode :

What is Poseview ?

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Image generated by PoseView

Protein

Binding Site

Ligand

Interaction pattern

hydrophobic (CA)

aromatic (CZ)

hydrogen bond acceptor (O)

hydrogen bond acceptor/donor (OG)

hydrogen bond donor (N)

positively ionized (NZ)

negatively ionized (OD1)

metal (ZN)

Legend:

Represent the protein/ligand binding mode, centered on the ligand
Dashed lines represents hydrogen bonds and metal interactions
Green residue labels for amino acids with hydrophobic contacts (green lines) to the ligand

Image generated using PoseView by BioSolveIT

Ligand	Protein		Interaction
Atom	Atom	Residue	Distance (Å)	Angle (°)	Type
O36	N	ASP- 43	2.93	172.46	H-Bond (Protein Donor)	false
O26	NZ	LYS- 46	3.76	0	Ionic (Protein Cationic)	false
O36	NZ	LYS- 46	2.54	0	Ionic (Protein Cationic)	false
O36	NZ	LYS- 46	2.54	140.77	H-Bond (Protein Donor)	false
O3A	ND2	ASN- 68	3.02	166.47	H-Bond (Protein Donor)	false
O16	N	GLY- 70	2.95	155.59	H-Bond (Protein Donor)	false
O26	NE2	HIS- 71	2.56	144.58	H-Bond (Protein Donor)	false
C5'	CG2	ILE- 160	3.99	0	Hydrophobic	false
O1A	N	THR- 163	2.84	160.04	H-Bond (Protein Donor)	false
O26	N	ASN- 256	2.93	158.96	H-Bond (Protein Donor)	false
N7	ND2	ASN- 256	2.77	149.6	H-Bond (Protein Donor)	false
C4'	CD2	LEU- 260	4.31	0	Hydrophobic	false
C1'	CD1	LEU- 260	3.68	0	Hydrophobic	false
O3A	OG1	THR- 271	2.57	156.87	H-Bond (Protein Donor)	false
C5'	CB	THR- 271	4.4	0	Hydrophobic	false
C2'	CB	VAL- 305	4.29	0	Hydrophobic	false
N3	O	HOH- 509	2.57	154.33	H-Bond (Protein Donor)	false
O1A	O	HOH- 532	2.68	179.95	H-Bond (Protein Donor)	false
O16	MG	MG- 1454	2.04	0	Metal Acceptor	false