scPDB - 3cem entry

Protein Data Bank Entry:

PDB ID : 3cem

Resolution :2.470 Å

Experimental Method : X-ray

Deposition Date : 2008-02-29

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	79 %
B	21 %

Ligand binding site composition:

B-Factor:	27.980
Number of residues:	35
Including
Standard Amino Acids:	34
Non Standard Amino Acids:	0
Water Molecules:	1
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.648	570.375

% Hydrophobic	% Polar
56.80	43.20
According to VolSite

Ligand :

HET Code:	AVD
Formula:	C23H10Cl2F2N2O5
Molecular weight:	503.239 g/mol
DrugBank ID:	-
Buried Surface Area:	66.22 %
Polar Surface area:	112.6 Å2

Number of
H-Bond Acceptors:	7
H-Bond Donors:	1
Rings:	4
Aromatic rings:	3
Anionic atoms:	2
Cationic atoms:	0
Rule of Five Violation:	1
Rotatable Bonds:	5

Mass center Coordinates

X	Y	Z
35.0562	101.067	134.634

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
N10	O	VAL- 40	2.76	122.76	H-Bond (Ligand Donor)	false
CL12	CG1	VAL- 40	4.15	0	Hydrophobic	false
C5	CB	VAL- 40	3.86	0	Hydrophobic	false
C3	CG1	VAL- 40	3.51	0	Hydrophobic	false
C1	CB	VAL- 40	3.62	0	Hydrophobic	false
F9	CD	LYS- 41	3.23	0	Hydrophobic	false
CL29	CG2	VAL- 45	3.51	0	Hydrophobic	false
C15	CG2	VAL- 45	3.95	0	Hydrophobic	false
C33	CG1	VAL- 45	3.46	0	Hydrophobic	false
CL12	CD2	TRP- 67	3.77	0	Hydrophobic	false
F11	CH2	TRP- 67	3.46	0	Hydrophobic	false
CL29	CG2	ILE- 68	3.84	0	Hydrophobic	false
CL12	CG	GLN- 71	3.54	0	Hydrophobic	false
C16	CB	GLN- 71	4.03	0	Hydrophobic	false
C17	CG	GLN- 71	4.07	0	Hydrophobic	false
C31	CG	TYR- 75	3.46	0	Hydrophobic	false
F11	CG	LYS- 191	3.51	0	Hydrophobic	false
O25	NH1	ARG- 193	3.02	168.14	H-Bond (Protein Donor)	false
C6	CD	ARG- 193	3.73	0	Hydrophobic	false
F11	CB	ASP- 227	3.69	0	Hydrophobic	false
O27	NH2	ARG- 242	3.05	133.5	H-Bond (Protein Donor)	false
O27	NH1	ARG- 242	3.07	133.43	H-Bond (Protein Donor)	false
O25	NH2	ARG- 242	3.01	126.01	H-Bond (Protein Donor)	false
O27	CZ	ARG- 242	3.45	0	Ionic (Protein Cationic)	false
O42	CZ	ARG- 309	3.68	0	Ionic (Protein Cationic)	false
O42	NH1	ARG- 309	3.17	154.4	H-Bond (Protein Donor)	false
O42	NH2	ARG- 309	3.27	148.28	H-Bond (Protein Donor)	false
O27	NH2	ARG- 309	3.43	143.84	H-Bond (Protein Donor)	false
O42	NE	ARG- 310	2.92	150.8	H-Bond (Protein Donor)	false
O27	NH2	ARG- 310	3.03	172.84	H-Bond (Protein Donor)	false
O42	CZ	ARG- 310	3.73	0	Ionic (Protein Cationic)	false
O27	CZ	ARG- 310	3.86	0	Ionic (Protein Cationic)	false