scPDB - 4aza entry

Protein Data Bank Entry:

PDB ID : 4aza

Resolution :2.160 Å

Experimental Method : X-ray

Deposition Date : 2012-06-25

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
ID:	IF4E_HUMAN
AC:	P06730
Organism:	Homo sapiens
Reign:	Eukaryota
TaxID:	9606
EC Number:	/

Chains:

Chain Name:	Percentage of Residues within binding site
A	67 %
C	33 %

Ligand binding site composition:

B-Factor:	12.004
Number of residues:	29
Including
Standard Amino Acids:	27
Non Standard Amino Acids:	0
Water Molecules:	2
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.190	853.875

% Hydrophobic	% Polar
35.18	64.82
According to VolSite

Ligand :

HET Code:	MGO
Formula:	C12H16N4O14P3
Molecular weight:	533.195 g/mol
DrugBank ID:	-
Buried Surface Area:	49.15 %
Polar Surface area:	314.19 Å2

Number of
H-Bond Acceptors:	15
H-Bond Donors:	4
Rings:	3
Aromatic rings:	1
Anionic atoms:	4
Cationic atoms:	1
Rule of Five Violation:	2
Rotatable Bonds:	8

Mass center Coordinates

X	Y	Z
-16.3563	3.13718	-24.7142

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
CAA	CZ2	TRP- 56	3.37	0	Hydrophobic	false
DuAr	DuAr	TRP- 56	3.52	0	Aromatic Face/Face	false
CAA	CE2	TRP- 102	3.99	0	Hydrophobic	false
C2'	CH2	TRP- 102	3.85	0	Hydrophobic	false
OAC	N	TRP- 102	2.89	157.69	H-Bond (Protein Donor)	false
DuAr	DuAr	TRP- 102	3.9	0	Aromatic Face/Face	false
NAB	OE2	GLU- 103	2.73	129.58	H-Bond (Ligand Donor)	false
NAP	OE1	GLU- 103	2.69	174.75	H-Bond (Ligand Donor)	false
OAL	CZ	ARG- 157	3.48	0	Ionic (Protein Cationic)	false
OAE	CZ	ARG- 157	3.81	0	Ionic (Protein Cationic)	false
OAL	NH2	ARG- 157	3.43	127.79	H-Bond (Protein Donor)	false
OAL	NE	ARG- 157	2.69	177.55	H-Bond (Protein Donor)	false
OAE	NH2	ARG- 157	2.77	153.64	H-Bond (Protein Donor)	false
OAI	NZ	LYS- 159	3.66	0	Ionic (Protein Cationic)	false
OAF	NZ	LYS- 159	3.14	0	Ionic (Protein Cationic)	false
OAF	NZ	LYS- 159	3.14	133.32	H-Bond (Protein Donor)	false
OAD	NZ	LYS- 162	2.62	0	Ionic (Protein Cationic)	false
OAF	NZ	LYS- 162	2.58	0	Ionic (Protein Cationic)	false
OAF	NZ	LYS- 162	2.58	165.85	H-Bond (Protein Donor)	false
CAA	CH2	TRP- 166	4.04	0	Hydrophobic	false
OAE	O	HOH- 2019	2.69	163.6	H-Bond (Protein Donor)	false
OAK	O	HOH- 2049	2.93	172.16	H-Bond (Protein Donor)	false