scPDB - 3u2x entry

Protein Data Bank Entry:

PDB ID : 3u2x

Resolution :1.770 Å

Experimental Method : X-ray

Deposition Date : 2011-10-04

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Glycogenin-1
ID:	GLYG_HUMAN
AC:	P46976
Organism:	Homo sapiens
Reign:	Eukaryota
TaxID:	9606
EC Number:	2.4.1.186

Chains:

Chain Name:	Percentage of Residues within binding site
A	96 %
B	4 %

Ligand binding site composition:

B-Factor:	20.881
Number of residues:	27
Including
Standard Amino Acids:	25
Non Standard Amino Acids:	2
Water Molecules:	0
Cofactors:
Metals:	MN

Cavity properties

Ligandability	Volume (Å3)
1.311	1049.625

% Hydrophobic	% Polar
49.84	50.16
According to VolSite

Ligand :

HET Code:	ASO
Formula:	C6H12O5
Molecular weight:	164.156 g/mol
DrugBank ID:	-
Buried Surface Area:	85.99 %
Polar Surface area:	90.15 Å2

Number of
H-Bond Acceptors:	5
H-Bond Donors:	4
Rings:	1
Aromatic rings:	0
Anionic atoms:	0
Cationic atoms:	0
Rule of Five Violation:	0
Rotatable Bonds:	1

Mass center Coordinates

X	Y	Z
55.214	24.6501	21.5199

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
C6	SD	MET- 75	4.02	0	Hydrophobic	false
C6	CD1	LEU- 80	4.21	0	Hydrophobic	false
O3	NZ	LYS- 86	2.63	124.5	H-Bond (Protein Donor)	false
O3	OD1	ASP- 102	3.1	124.43	H-Bond (Ligand Donor)	false
O3	OD2	ASP- 102	2.97	157.22	H-Bond (Ligand Donor)	false
C2	CB	SER- 134	4.46	0	Hydrophobic	false
O6	OD2	ASP- 160	2.82	161.96	H-Bond (Ligand Donor)	false
O4	OD1	ASP- 163	2.71	150.88	H-Bond (Ligand Donor)	false
O6	N	GLN- 164	3.13	152.17	H-Bond (Protein Donor)	false
C6	CB	GLN- 164	4.06	0	Hydrophobic	false
C1	CD1	LEU- 214	4.24	0	Hydrophobic	false