scPDB - 3t7o entry

Protein Data Bank Entry:

PDB ID : 3t7o

Resolution :1.850 Å

Experimental Method : X-ray

Deposition Date : 2011-07-30

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	98 %
B	2 %

Ligand binding site composition:

B-Factor:	20.037
Number of residues:	44
Including
Standard Amino Acids:	41
Non Standard Amino Acids:	2
Water Molecules:	1
Cofactors:
Metals:	MN

Cavity properties

Ligandability	Volume (Å3)
0.407	2143.125

% Hydrophobic	% Polar
44.88	55.12
According to VolSite

Ligand :

HET Code:	UPG
Formula:	C15H22N2O17P2
Molecular weight:	564.286 g/mol
DrugBank ID:	DB01861
Buried Surface Area:	81.74 %
Polar Surface area:	316.82 Å2

Number of
H-Bond Acceptors:	17
H-Bond Donors:	7
Rings:	3
Aromatic rings:	0
Anionic atoms:	2
Cationic atoms:	0
Rule of Five Violation:	3
Rotatable Bonds:	9

Mass center Coordinates

X	Y	Z
38.82	20.7567	22.6769

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
C1C	CD2	LEU- 9	3.95	0	Hydrophobic	false
O2C	O	LEU- 9	2.78	173.89	H-Bond (Ligand Donor)	false
N3	OG1	THR- 11	2.65	139.21	H-Bond (Ligand Donor)	false
O2	N	THR- 11	2.95	134.41	H-Bond (Protein Donor)	false
C3C	CE2	TYR- 15	3.54	0	Hydrophobic	false
C2C	CD2	TYR- 15	3.54	0	Hydrophobic	false
O2A	OH	TYR- 15	2.69	146.19	H-Bond (Protein Donor)	false
C6'	CE	MET- 75	4.25	0	Hydrophobic	false
O2A	NH2	ARG- 77	3.13	137.09	H-Bond (Protein Donor)	false
O2B	NH2	ARG- 77	3.28	136.97	H-Bond (Protein Donor)	false
O2B	NH1	ARG- 77	2.9	156.69	H-Bond (Protein Donor)	false
O3B	NH1	ARG- 77	3.38	135.7	H-Bond (Protein Donor)	false
O2B	CZ	ARG- 77	3.53	0	Ionic (Protein Cationic)	false
C5'	CD1	LEU- 80	4.11	0	Hydrophobic	false
C5C	CG2	THR- 83	3.75	0	Hydrophobic	false
O4'	NZ	LYS- 86	3.39	150.11	H-Bond (Protein Donor)	false
C3C	CB	ASP- 102	4.47	0	Hydrophobic	false
C2C	CB	ALA- 103	3.88	0	Hydrophobic	false
O2C	N	ALA- 103	3.25	164.38	H-Bond (Protein Donor)	false
O3C	OD1	ASP- 104	3.03	122.21	H-Bond (Ligand Donor)	false
O2'	ND2	ASN- 133	3.04	140.86	H-Bond (Protein Donor)	false
O3'	OG	SER- 134	2.97	161.86	H-Bond (Ligand Donor)	false
O6'	OD1	ASP- 160	3.35	150.69	H-Bond (Ligand Donor)	false
O6'	OD2	ASP- 160	2.91	147.16	H-Bond (Ligand Donor)	false
C6'	CB	GLN- 164	3.38	0	Hydrophobic	false
C4'	CB	GLN- 164	4.19	0	Hydrophobic	false
O6'	N	GLN- 164	2.94	156.08	H-Bond (Protein Donor)	false
O2B	N	GLY- 215	2.95	163.41	H-Bond (Protein Donor)	false
O1A	NZ	LYS- 218	3.53	0	Ionic (Protein Cationic)	false
O2A	NZ	LYS- 218	3.27	0	Ionic (Protein Cationic)	false
O2B	NZ	LYS- 218	2.79	0	Ionic (Protein Cationic)	false
O2B	NZ	LYS- 218	2.79	144.47	H-Bond (Protein Donor)	false
O1A	MN	MN- 264	1.97	0	Metal Acceptor	false
O1B	MN	MN- 264	1.98	0	Metal Acceptor	false