scPDB - 4el0 entry

Protein Data Bank Entry:

PDB ID : 4el0

Resolution :2.400 Å

Experimental Method : X-ray

Deposition Date : 2012-04-10

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Glycogen phosphorylase, muscle form
ID:	PYGM_RABIT
AC:	P00489
Organism:	Oryctolagus cuniculus
Reign:	Eukaryota
TaxID:	9986
EC Number:	2.4.1.1

Chains:

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

Ligand binding site composition:

B-Factor:	17.975
Number of residues:	41
Including
Standard Amino Acids:	35
Non Standard Amino Acids:	1
Water Molecules:	5
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.011	388.125

% Hydrophobic	% Polar
31.30	68.70
According to VolSite

Ligand :

HET Code:	D1K
Formula:	C15H20N2O7
Molecular weight:	340.328 g/mol
DrugBank ID:	-
Buried Surface Area:	71.23 %
Polar Surface area:	132.05 Å2

Number of
H-Bond Acceptors:	8
H-Bond Donors:	4
Rings:	3
Aromatic rings:	0
Anionic atoms:	0
Cationic atoms:	0
Rule of Five Violation:	0
Rotatable Bonds:	4

Mass center Coordinates

X	Y	Z
34.7319	23.0208	28.7892

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
O2	N	LEU- 136	3.04	155.16	H-Bond (Protein Donor)	false
C6'	CD2	LEU- 139	4.1	0	Hydrophobic	false
C10	CB	ASP- 339	4.07	0	Hydrophobic	false
O6'	ND1	HIS- 377	2.73	150.93	H-Bond (Ligand Donor)	false
C11	CG	GLU- 385	3.98	0	Hydrophobic	false
O4'	ND2	ASN- 484	3.49	129.65	H-Bond (Protein Donor)	false
O6'	ND2	ASN- 484	2.66	156.93	H-Bond (Protein Donor)	false
O3'	OE1	GLU- 672	2.76	161.74	H-Bond (Ligand Donor)	false
O3'	N	SER- 674	2.99	174.71	H-Bond (Protein Donor)	false
C4'	CB	SER- 674	4.14	0	Hydrophobic	false
O3'	N	GLY- 675	3.06	142.21	H-Bond (Protein Donor)	false
O4'	N	GLY- 675	2.59	125.13	H-Bond (Protein Donor)	false
O4'	O	HOH- 1112	2.59	158.19	H-Bond (Ligand Donor)	false
O2'	O	HOH- 1199	2.75	171.88	H-Bond (Ligand Donor)	false