scPDB - 3fqj entry

Protein Data Bank Entry:

PDB ID : 3fqj

Resolution :2.620 Å

Experimental Method : X-ray

Deposition Date : 2009-01-07

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Decapping and exoribonuclease protein
ID:	DXO_MOUSE
AC:	O70348
Organism:	Mus musculus
Reign:	Eukaryota
TaxID:	10090
EC Number:	3.1.13

Chains:

Chain Name:	Percentage of Residues within binding site
A	100 %

Ligand binding site composition:

B-Factor:	23.800
Number of residues:	33
Including
Standard Amino Acids:	30
Non Standard Amino Acids:	1
Water Molecules:	2
Cofactors:
Metals:	MG

Cavity properties

Ligandability	Volume (Å3)
0.937	1130.625

% Hydrophobic	% Polar
38.51	61.49
According to VolSite

Ligand :

HET Code:	GDP
Formula:	C10H12N5O11P2
Molecular weight:	440.177 g/mol
DrugBank ID:	DB04315
Buried Surface Area:	49.89 %
Polar Surface area:	276.39 Å2

Number of
H-Bond Acceptors:	14
H-Bond Donors:	4
Rings:	3
Aromatic rings:	1
Anionic atoms:	3
Cationic atoms:	0
Rule of Five Violation:	1
Rotatable Bonds:	6

Mass center Coordinates

X	Y	Z
-4.48893	-26.7842	19.9785

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'	NH2	ARG- 58	2.86	153.68	H-Bond (Protein Donor)	false
O2'	NH1	ARG- 58	3.49	128.46	H-Bond (Protein Donor)	false
N2	OE1	GLU- 101	3.08	147.94	H-Bond (Ligand Donor)	false
N3	OE1	GLU- 101	3.24	141.28	H-Bond (Ligand Donor)	false
C5'	CE3	TRP- 131	3.21	0	Hydrophobic	false
O1B	NE	ARG- 132	2.67	133.72	H-Bond (Protein Donor)	false
O1B	NH2	ARG- 132	3.02	122.52	H-Bond (Protein Donor)	false
O2A	NE	ARG- 132	3.25	120.35	H-Bond (Protein Donor)	false
O2A	NH2	ARG- 132	2.8	127.33	H-Bond (Protein Donor)	false
O1B	CZ	ARG- 132	3.21	0	Ionic (Protein Cationic)	false
O2A	CZ	ARG- 132	3.37	0	Ionic (Protein Cationic)	false
O1A	N	GLY- 133	2.82	140.8	H-Bond (Protein Donor)	false
C3'	SG	CYS- 217	3.49	0	Hydrophobic	false
O2A	N	GLU- 234	2.96	149.85	H-Bond (Protein Donor)	false
C3'	CB	GLU- 234	4.44	0	Hydrophobic	false
O1B	NE2	GLN- 280	3.23	156.16	H-Bond (Protein Donor)	false
O2'	O	HOH- 487	2.95	139.96	H-Bond (Ligand Donor)	false