scPDB - 3t3i entry

Protein Data Bank Entry:

PDB ID : 3t3i

Resolution :2.650 Å

Experimental Method : X-ray

Deposition Date : 2011-07-25

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:	17.215
Number of residues:	37
Including
Standard Amino Acids:	34
Non Standard Amino Acids:	1
Water Molecules:	2
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.738	533.250

% Hydrophobic	% Polar
48.73	51.27
According to VolSite

Ligand :

HET Code:	GPW
Formula:	C11H13F3N2O7
Molecular weight:	342.225 g/mol
DrugBank ID:	-
Buried Surface Area:	77.52 %
Polar Surface area:	139.56 Å2

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

Mass center Coordinates

X	Y	Z
34.4359	22.9822	28.5337

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
O2	N	LEU- 136	3.19	147.92	H-Bond (Protein Donor)	false
C1'	CB	LEU- 136	4.1	0	Hydrophobic	false
C6'	CB	LEU- 136	4.47	0	Hydrophobic	false
F2	CD1	LEU- 136	3.76	0	Hydrophobic	false
C6'	CB	LEU- 139	4.18	0	Hydrophobic	false
N3	OD1	ASP- 283	2.73	162.68	H-Bond (Ligand Donor)	false
F1	CB	ASN- 284	4.38	0	Hydrophobic	false
O4	N	ASN- 284	2.94	158.45	H-Bond (Protein Donor)	false
O2'	ND2	ASN- 284	3.47	158.05	H-Bond (Protein Donor)	false
F2	CB	ASP- 339	4.34	0	Hydrophobic	false
C7	CB	HIS- 377	4.22	0	Hydrophobic	false
F1	CG2	THR- 378	3.6	0	Hydrophobic	false
F3	CB	THR- 378	3.49	0	Hydrophobic	false
F1	CB	ALA- 383	3.62	0	Hydrophobic	false
O4'	ND2	ASN- 484	3.39	125.91	H-Bond (Protein Donor)	false
O2'	OE1	GLU- 672	3.12	157.6	H-Bond (Ligand Donor)	false
O3'	OE1	GLU- 672	2.68	156.87	H-Bond (Ligand Donor)	false
O3'	N	SER- 674	2.93	167.89	H-Bond (Protein Donor)	false
C4'	CB	SER- 674	4.31	0	Hydrophobic	false
O3'	N	GLY- 675	3.15	145.68	H-Bond (Protein Donor)	false
O4'	N	GLY- 675	2.84	129.83	H-Bond (Protein Donor)	false