scPDB - 3dds entry

Protein Data Bank Entry:

PDB ID : 3dds

Resolution :1.800 Å

Experimental Method : X-ray

Deposition Date : 2008-06-06

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Glycogen phosphorylase, liver form
ID:	PYGL_HUMAN
AC:	P06737
Organism:	Homo sapiens
Reign:	Eukaryota
TaxID:	9606
EC Number:	2.4.1.1

Chains:

Chain Name:	Percentage of Residues within binding site
A	23 %
B	77 %

Ligand binding site composition:

B-Factor:	29.432
Number of residues:	33
Including
Standard Amino Acids:	31
Non Standard Amino Acids:	0
Water Molecules:	2
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.827	708.750

% Hydrophobic	% Polar
50.00	50.00
According to VolSite

Ligand :

HET Code:	26B
Formula:	C29H34N3O5
Molecular weight:	504.597 g/mol
DrugBank ID:	-
Buried Surface Area:	63.76 %
Polar Surface area:	119.58 Å2

Number of
H-Bond Acceptors:	5
H-Bond Donors:	3
Rings:	3
Aromatic rings:	3
Anionic atoms:	1
Cationic atoms:	0
Rule of Five Violation:	1
Rotatable Bonds:	8

Mass center Coordinates

X	Y	Z
105.963	-91.6249	93.0359

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
N23	O	VAL- 40	3.01	162.3	H-Bond (Ligand Donor)	false
C32	CG1	VAL- 40	4.14	0	Hydrophobic	false
C26	CD	LYS- 41	3.9	0	Hydrophobic	false
O22	N	ASP- 42	2.87	174.19	H-Bond (Protein Donor)	false
C18	CB	ASP- 42	4.01	0	Hydrophobic	false
C1	CB	VAL- 45	4.42	0	Hydrophobic	false
C18	CG2	VAL- 45	3.94	0	Hydrophobic	false
C26	CG2	VAL- 45	4.5	0	Hydrophobic	false
C12	CG1	VAL- 45	3.9	0	Hydrophobic	false
C32	CD2	TRP- 67	4.03	0	Hydrophobic	false
C18	CG2	ILE- 68	4.44	0	Hydrophobic	false
C32	CG1	ILE- 68	4.02	0	Hydrophobic	false
C18	CB	GLN- 71	4.08	0	Hydrophobic	false
C10	CB	GLN- 71	3.7	0	Hydrophobic	false
C31	CG	GLN- 71	3.64	0	Hydrophobic	false
C15	CG	GLN- 72	3.65	0	Hydrophobic	false
C16	CB	GLN- 72	3.91	0	Hydrophobic	false
C13	CB	TYR- 75	3.96	0	Hydrophobic	false
C26	CD	ARG- 193	4.45	0	Hydrophobic	false
C27	CD	ARG- 193	4.33	0	Hydrophobic	false
DuAr	CZ	ARG- 193	3.81	16.26	Pi/Cation	false
C1	CZ	PHE- 196	3.48	0	Hydrophobic	false
C2	CE1	PHE- 196	3.96	0	Hydrophobic	false
C5	CE1	PHE- 196	3.87	0	Hydrophobic	false
C26	CE2	PHE- 196	4.08	0	Hydrophobic	false
C29	CB	ASP- 227	4.43	0	Hydrophobic	false
C29	CG2	THR- 240	3.8	0	Hydrophobic	false
C5	CG	ARG- 309	4.28	0	Hydrophobic	false
C7	CG	ARG- 309	4.4	0	Hydrophobic	false
O	NE	ARG- 310	3.03	166.44	H-Bond (Protein Donor)	false
OXT	NH2	ARG- 310	2.9	161.34	H-Bond (Protein Donor)	false
OXT	NE	ARG- 310	3.4	138.11	H-Bond (Protein Donor)	false
O	CZ	ARG- 310	3.96	0	Ionic (Protein Cationic)	false
OXT	CZ	ARG- 310	3.6	0	Ionic (Protein Cationic)	false
C7	CB	ARG- 310	3.9	0	Hydrophobic	false
C6	CB	ALA- 313	3.28	0	Hydrophobic	false
OXT	O	HOH- 938	2.65	179.98	H-Bond (Protein Donor)	false