scPDB - 3epx entry

Protein Data Bank Entry:

PDB ID : 3epx

Resolution :1.850 Å

Experimental Method : X-ray

Deposition Date : 2008-09-30

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	IAG-nucleoside hydrolase
ID:	Q9GPQ4_TRYVI
AC:	Q9GPQ4
Organism:	Trypanosoma vivax
Reign:	Eukaryota
TaxID:	5699
EC Number:	/

Chains:

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

Ligand binding site composition:

B-Factor:	18.381
Number of residues:	31
Including
Standard Amino Acids:	28
Non Standard Amino Acids:	1
Water Molecules:	2
Cofactors:
Metals:	CA

Cavity properties

Ligandability	Volume (Å3)
0.343	334.125

% Hydrophobic	% Polar
49.49	50.51
According to VolSite

Ligand :

HET Code:	IMQ
Formula:	C15H19N2O3
Molecular weight:	275.323 g/mol
DrugBank ID:	-
Buried Surface Area:	83.61 %
Polar Surface area:	78.02 Å2

Number of
H-Bond Acceptors:	4
H-Bond Donors:	4
Rings:	3
Aromatic rings:	2
Anionic atoms:	0
Cationic atoms:	1
Rule of Five Violation:	0
Rotatable Bonds:	3

Mass center Coordinates

X	Y	Z
43.8963	21.9702	41.6845

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'	OD1	ASP- 14	2.56	161.28	H-Bond (Ligand Donor)	false
N1	OD2	ASP- 40	2.74	161.24	H-Bond (Ligand Donor)	false
N4'	OD2	ASP- 40	3.35	0	Ionic (Ligand Cationic)	false
C2	CB	TRP- 83	3.86	0	Hydrophobic	false
DuAr	DuAr	TRP- 83	3.64	0	Aromatic Face/Face	false
DuAr	DuAr	TRP- 83	3.84	0	Aromatic Face/Face	false
C3'	SD	MET- 164	3.88	0	Hydrophobic	false
C5'	SD	MET- 164	4.02	0	Hydrophobic	false
O5'	ND2	ASN- 173	3.05	159.6	H-Bond (Protein Donor)	false
O5'	OE2	GLU- 184	2.54	157.02	H-Bond (Ligand Donor)	false
C7	CB	TRP- 185	4.37	0	Hydrophobic	false
O3'	ND2	ASN- 186	3.02	159.21	H-Bond (Protein Donor)	false
C5'	CD2	TRP- 260	3.68	0	Hydrophobic	false
C2'	CE3	TRP- 260	3.28	0	Hydrophobic	false
O3'	OD1	ASP- 261	2.69	175.31	H-Bond (Ligand Donor)	false
O2'	CA	CA- 1001	2.44	0	Metal Acceptor	false
O3'	CA	CA- 1001	2.48	0	Metal Acceptor	false
N4'	O	HOH- 1027	3.11	155.01	H-Bond (Ligand Donor)	false