scPDB - 1kie entry

Protein Data Bank Entry:

PDB ID : 1kie

Resolution :2.000 Å

Experimental Method : X-ray

Deposition Date : 2001-12-03

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
B	100 %

Ligand binding site composition:

B-Factor:	30.600
Number of residues:	25
Including
Standard Amino Acids:	24
Non Standard Amino Acids:	1
Water Molecules:	0
Cofactors:
Metals:	CA

Cavity properties

Ligandability	Volume (Å3)
0.258	354.375

% Hydrophobic	% Polar
54.29	45.71
According to VolSite

Ligand :

HET Code:	AD3
Formula:	C11H14N4O4
Molecular weight:	266.253 g/mol
DrugBank ID:	DB04546
Buried Surface Area:	74.64 %
Polar Surface area:	126.65 Å2

Number of
H-Bond Acceptors:	7
H-Bond Donors:	4
Rings:	3
Aromatic rings:	2
Anionic atoms:	0
Cationic atoms:	0
Rule of Five Violation:	0
Rotatable Bonds:	2

Mass center Coordinates

X	Y	Z
16.0745	5.93537	49.9365

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'	OD2	ASP- 14	2.62	152.97	H-Bond (Ligand Donor)	false
C1'	CH2	TRP- 83	3.84	0	Hydrophobic	false
C5'	SD	MET- 164	3.52	0	Hydrophobic	false
O5'	ND2	ASN- 173	2.75	171.93	H-Bond (Protein Donor)	false
O5'	OE1	GLU- 184	2.54	161.12	H-Bond (Ligand Donor)	false
C5'	CG	GLU- 184	4.43	0	Hydrophobic	false
C3	CB	TRP- 185	4.37	0	Hydrophobic	false
O3'	ND2	ASN- 186	3.02	141.93	H-Bond (Protein Donor)	false
C5'	CD2	TRP- 260	3.84	0	Hydrophobic	false
C3'	CB	TRP- 260	3.81	0	Hydrophobic	false
C2'	CE3	TRP- 260	3.89	0	Hydrophobic	false
O3'	OD2	ASP- 261	3.09	122.5	H-Bond (Ligand Donor)	false
O3'	CA	CA- 328	2.72	0	Metal Acceptor	false