scPDB - 1zdf entry

Protein Data Bank Entry:

PDB ID : 1zdf

Resolution :2.450 Å

Experimental Method : X-ray

Deposition Date : 2005-04-14

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_RABIT
AC:	P13280
Organism:	Oryctolagus cuniculus
Reign:	Eukaryota
TaxID:	9986
EC Number:	2.4.1.186

Chains:

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

Ligand binding site composition:

B-Factor:	33.322
Number of residues:	36
Including
Standard Amino Acids:	34
Non Standard Amino Acids:	1
Water Molecules:	1
Cofactors:
Metals:	MN

Cavity properties

Ligandability	Volume (Å3)
0.203	391.500

% Hydrophobic	% Polar
37.07	62.93
According to VolSite

Ligand :

HET Code:	UPG
Formula:	C15H22N2O17P2
Molecular weight:	564.286 g/mol
DrugBank ID:	DB01861
Buried Surface Area:	60.34 %
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
5.12692	-36.3542	85.7639

Binding mode :

What is Poseview ?

2D View
3D View

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- 8	3.96	0	Hydrophobic	false
O2C	O	LEU- 8	2.72	166.55	H-Bond (Ligand Donor)	false
N3	OG1	THR- 10	2.69	132.88	H-Bond (Ligand Donor)	false
O2	N	THR- 10	2.95	135.6	H-Bond (Protein Donor)	false
C3C	CE2	TYR- 14	3.67	0	Hydrophobic	false
C2C	CD2	TYR- 14	3.56	0	Hydrophobic	false
C1C	CG1	VAL- 81	4.27	0	Hydrophobic	false
O6'	OD2	ASP- 101	3.13	161.3	H-Bond (Ligand Donor)	false
C3C	CB	ASP- 101	4.1	0	Hydrophobic	false
C2C	CB	ALA- 102	3.9	0	Hydrophobic	false
O2C	N	ALA- 102	2.98	167.06	H-Bond (Protein Donor)	false
O3C	OD1	ASP- 103	2.89	128.46	H-Bond (Ligand Donor)	false
O3C	N	ASP- 103	3.42	145.66	H-Bond (Protein Donor)	false
C6'	CB	SER- 133	4.16	0	Hydrophobic	false
C4'	CB	GLN- 163	4.37	0	Hydrophobic	false
O4'	OE1	GLN- 163	2.58	153.34	H-Bond (Ligand Donor)	false
C5'	CD2	LEU- 213	4.07	0	Hydrophobic	false
O1A	NZ	LYS- 217	3.69	0	Ionic (Protein Cationic)	false
O2A	NZ	LYS- 217	3.98	0	Ionic (Protein Cationic)	false
O1B	NZ	LYS- 217	3.84	0	Ionic (Protein Cationic)	false
O2B	NZ	LYS- 217	2.9	0	Ionic (Protein Cationic)	false
O2B	NZ	LYS- 217	2.9	131.99	H-Bond (Protein Donor)	false
O1A	MN	MN- 400	2.33	0	Metal Acceptor	false
O1B	MN	MN- 400	2.01	0	Metal Acceptor	false
O5'	O	HOH- 431	3.48	163.01	H-Bond (Protein Donor)	false