scPDB - 2jgb entry

Protein Data Bank Entry:

PDB ID : 2jgb

Resolution :1.700 Å

Experimental Method : X-ray

Deposition Date : 2007-02-12

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Eukaryotic translation initiation factor 4E type 2
ID:	IF4E2_HUMAN
AC:	O60573
Organism:	Homo sapiens
Reign:	Eukaryota
TaxID:	9606
EC Number:	/

Chains:

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

Ligand binding site composition:

B-Factor:	22.376
Number of residues:	30
Including
Standard Amino Acids:	29
Non Standard Amino Acids:	0
Water Molecules:	1
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.059	732.375

% Hydrophobic	% Polar
37.79	62.21
According to VolSite

Ligand :

HET Code:	MGT
Formula:	C11H16N5O14P3
Molecular weight:	535.191 g/mol
DrugBank ID:	DB03358
Buried Surface Area:	48.55 %
Polar Surface area:	324.22 Å2

Number of
H-Bond Acceptors:	18
H-Bond Donors:	4
Rings:	3
Aromatic rings:	0
Anionic atoms:	4
Cationic atoms:	0
Rule of Five Violation:	2
Rotatable Bonds:	8

Mass center Coordinates

X	Y	Z
-16.0097	11.3099	15.4852

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
C5'	CD	ARG- 67	3.99	0	Hydrophobic	false
C4'	CB	THR- 73	4.17	0	Hydrophobic	false
C5'	CE1	TYR- 78	4.4	0	Hydrophobic	false
CM7	CZ	TYR- 78	3.85	0	Hydrophobic	false
DuAr	DuAr	TYR- 78	4	0	Aromatic Face/Face	false
O1A	NE2	HIS- 110	2.65	172.61	H-Bond (Protein Donor)	false
C2'	CH2	TRP- 124	4.05	0	Hydrophobic	false
CM7	CE2	TRP- 124	3.86	0	Hydrophobic	false
O6	N	TRP- 124	2.71	158.56	H-Bond (Protein Donor)	false
DuAr	DuAr	TRP- 124	3.68	0	Aromatic Face/Face	false
N1	OE1	GLU- 125	2.73	172.42	H-Bond (Ligand Donor)	false
N1	OE2	GLU- 125	3.36	123.89	H-Bond (Ligand Donor)	false
N2	OE2	GLU- 125	2.65	146.17	H-Bond (Ligand Donor)	false
O2B	CZ	ARG- 174	3.27	0	Ionic (Protein Cationic)	false
O2B	NE	ARG- 174	2.82	148.69	H-Bond (Protein Donor)	false
O2B	NH2	ARG- 174	2.87	142.54	H-Bond (Protein Donor)	false
CM7	CH2	TRP- 183	3.93	0	Hydrophobic	false