scPDB - 2idv entry

Protein Data Bank Entry:

PDB ID : 2idv

Resolution :2.300 Å

Experimental Method : X-ray

Deposition Date : 2006-09-15

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-1
ID:	IF4E1_WHEAT
AC:	P29557
Organism:	Triticum aestivum
Reign:	Eukaryota
TaxID:	4565
EC Number:	/

Chains:

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

Ligand binding site composition:

B-Factor:	23.768
Number of residues:	21
Including
Standard Amino Acids:	20
Non Standard Amino Acids:	0
Water Molecules:	1
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.275	691.875

% Hydrophobic	% Polar
42.93	57.07
According to VolSite

Ligand :

HET Code:	M7G
Formula:	C11H16N5O11P2
Molecular weight:	456.219 g/mol
DrugBank ID:	DB01960
Buried Surface Area:	46.84 %
Polar Surface area:	265.04 Å2

Number of
H-Bond Acceptors:	15
H-Bond Donors:	4
Rings:	3
Aromatic rings:	0
Anionic atoms:	3
Cationic atoms:	0
Rule of Five Violation:	1
Rotatable Bonds:	6

Mass center Coordinates

X	Y	Z
2.83631	6.218	-3.28434

Binding mode :

What is Poseview ?

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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
O1A	CZ	ARG- 58	3.67	0	Ionic (Protein Cationic)	false
O1B	CZ	ARG- 58	3.5	0	Ionic (Protein Cationic)	false
O2B	CZ	ARG- 58	3.91	0	Ionic (Protein Cationic)	false
C5'	CB	ARG- 58	4.43	0	Hydrophobic	false
CM7	CZ2	TRP- 62	3.55	0	Hydrophobic	false
DuAr	DuAr	TRP- 62	3.56	0	Aromatic Face/Face	false
C3'	CH2	TRP- 108	4.15	0	Hydrophobic	false
C2'	CZ3	TRP- 108	4.18	0	Hydrophobic	false
CM7	CZ2	TRP- 108	3.51	0	Hydrophobic	false
O6	N	TRP- 108	2.99	168.32	H-Bond (Protein Donor)	false
DuAr	DuAr	TRP- 108	3.78	0	Aromatic Face/Face	false
N1	OE2	GLU- 109	3.02	138.04	H-Bond (Ligand Donor)	false
N2	OE2	GLU- 109	2.89	147.74	H-Bond (Ligand Donor)	false
O1A	NH2	ARG- 158	2.91	165.99	H-Bond (Protein Donor)	false
O2B	NE	ARG- 158	2.56	128.7	H-Bond (Protein Donor)	false
O1A	CZ	ARG- 158	3.81	0	Ionic (Protein Cationic)	false
O2B	CZ	ARG- 158	3.34	0	Ionic (Protein Cationic)	false
O2B	NH2	ARG- 163	3.18	163.5	H-Bond (Protein Donor)	false
O2A	O	HOH- 1031	3.37	166.49	H-Bond (Protein Donor)	false