scPDB - 2amv entry

Protein Data Bank Entry:

PDB ID : 2amv

Resolution :2.300 Å

Experimental Method : X-ray

Deposition Date : 1998-10-13

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:	25.489
Number of residues:	24
Including
Standard Amino Acids:	23
Non Standard Amino Acids:	0
Water Molecules:	1
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.007	543.375

% Hydrophobic	% Polar
46.58	53.42
According to VolSite

Ligand :

HET Code:	BIN
Formula:	C20H19ClNO6
Molecular weight:	404.821 g/mol
DrugBank ID:	DB04055
Buried Surface Area:	55.5 %
Polar Surface area:	110.44 Å2

Number of
H-Bond Acceptors:	6
H-Bond Donors:	0
Rings:	2
Aromatic rings:	2
Anionic atoms:	2
Cationic atoms:	1
Rule of Five Violation:	0
Rotatable Bonds:	7

Mass center Coordinates

X	Y	Z
28.0718	1.42043	51.796

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
C21	CE2	TRP- 67	4.38	0	Hydrophobic	false
C19	CG1	ILE- 68	3.46	0	Hydrophobic	false
C7	CB	GLN- 71	4.34	0	Hydrophobic	false
C15	CB	GLN- 71	4.34	0	Hydrophobic	false
C21	CG	GLN- 71	4.03	0	Hydrophobic	false
C15	CG	GLN- 72	3.44	0	Hydrophobic	false
C15	CB	TYR- 75	4.22	0	Hydrophobic	false
C17	CD1	TYR- 75	3.46	0	Hydrophobic	false
C3	CD	ARG- 193	4.15	0	Hydrophobic	false
CL2	CD	ARG- 193	3.9	0	Hydrophobic	false
C4	CG	GLU- 195	4.17	0	Hydrophobic	false
C5	CZ	PHE- 196	3.4	0	Hydrophobic	false
O3A	NH2	ARG- 242	3.12	143.66	H-Bond (Protein Donor)	false
O3A	CZ	ARG- 242	3.77	0	Ionic (Protein Cationic)	false
O3B	CZ	ARG- 309	3.89	0	Ionic (Protein Cationic)	false
O4A	NH2	ARG- 309	2.88	143.3	H-Bond (Protein Donor)	false
O3B	CZ	ARG- 310	3.8	0	Ionic (Protein Cationic)	false
O3B	NH1	ARG- 310	2.64	126.09	H-Bond (Protein Donor)	false