scPDB - 3ms4 entry

Protein Data Bank Entry:

PDB ID : 3ms4

Resolution :2.070 Å

Experimental Method : X-ray

Deposition Date : 2010-04-29

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Glycogen phosphorylase, 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:	36.736
Number of residues:	47
Including
Standard Amino Acids:	40
Non Standard Amino Acids:	1
Water Molecules:	6
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
1.018	955.125

% Hydrophobic	% Polar
40.64	59.36
According to VolSite

Ligand :

HET Code:	21N
Formula:	C15H18F3N3O5S
Molecular weight:	409.381 g/mol
DrugBank ID:	-
Buried Surface Area:	64.33 %
Polar Surface area:	158.66 Å2

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

Mass center Coordinates

X	Y	Z
34.858	24.3497	31.078

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
C1	CB	LEU- 136	4.45	0	Hydrophobic	false
C6	CD2	LEU- 139	4.05	0	Hydrophobic	false
F3	CB	TYR- 280	3.43	0	Hydrophobic	false
F1	CB	ASN- 282	4.08	0	Hydrophobic	false
C10	CB	ASP- 283	3.87	0	Hydrophobic	false
F2	CD	ARG- 292	4.46	0	Hydrophobic	false
C1	CB	HIS- 377	4.3	0	Hydrophobic	false
N1	O	HIS- 377	3.41	146.18	H-Bond (Ligand Donor)	false
O6	ND1	HIS- 377	2.75	169.52	H-Bond (Ligand Donor)	false
O4	ND2	ASN- 484	3.42	121.47	H-Bond (Protein Donor)	false
O6	ND2	ASN- 484	2.87	153.48	H-Bond (Protein Donor)	false
O3	OE1	GLU- 672	2.67	165.11	H-Bond (Ligand Donor)	false
C2	CB	ALA- 673	4.48	0	Hydrophobic	false
O3	N	SER- 674	3.03	173.7	H-Bond (Protein Donor)	false
C4	CB	SER- 674	4.26	0	Hydrophobic	false
O3	N	GLY- 675	3.1	146.21	H-Bond (Protein Donor)	false
O4	N	GLY- 675	2.78	124.86	H-Bond (Protein Donor)	false
O2	O	HOH- 943	2.95	177.49	H-Bond (Ligand Donor)	false