scPDB - 3iel entry

Protein Data Bank Entry:

PDB ID : 3iel

Resolution :2.350 Å

Experimental Method : X-ray

Deposition Date : 2009-07-23

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Ribonuclease TTHA0252
ID:	RNSE_THET8
AC:	Q5SLP1
Organism:	Thermus thermophilus
Reign:	Bacteria
TaxID:	300852
EC Number:	3.1

Chains:

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

Ligand binding site composition:

B-Factor:	38.669
Number of residues:	31
Including
Standard Amino Acids:	28
Non Standard Amino Acids:	2
Water Molecules:	1
Cofactors:
Metals:	ZN ZN

Cavity properties

Ligandability	Volume (Å3)
0.446	2031.750

% Hydrophobic	% Polar
51.99	48.01
According to VolSite

Ligand :

HET Code:	U5P
Formula:	C9H11N2O9P
Molecular weight:	322.165 g/mol
DrugBank ID:	-
Buried Surface Area:	66.34 %
Polar Surface area:	181.33 Å2

Number of
H-Bond Acceptors:	9
H-Bond Donors:	3
Rings:	2
Aromatic rings:	0
Anionic atoms:	2
Cationic atoms:	0
Rule of Five Violation:	1
Rotatable Bonds:	4

Mass center Coordinates

X	Y	Z
24.5406	-8.95505	35.9454

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
C2'	CG2	VAL- 12	4.23	0	Hydrophobic	false
C2'	CG2	THR- 188	4.14	0	Hydrophobic	false
O2P	OH	TYR- 189	2.55	127.41	H-Bond (Protein Donor)	false
C5'	CZ	PHE- 223	3.82	0	Hydrophobic	false
O1P	NH1	ARG- 227	2.67	173.08	H-Bond (Protein Donor)	false
O3P	NH2	ARG- 227	3.3	176.27	H-Bond (Protein Donor)	false
O1P	CZ	ARG- 227	3.53	0	Ionic (Protein Cationic)	false
C1'	CD1	TYR- 341	4.05	0	Hydrophobic	false
C5'	CB	TYR- 341	3.8	0	Hydrophobic	false
O3P	N	TYR- 341	2.85	167.66	H-Bond (Protein Donor)	false
O2P	OG	SER- 378	2.58	159.35	H-Bond (Protein Donor)	false
O1P	N	GLY- 379	2.89	169.17	H-Bond (Protein Donor)	false
N3	OE1	GLU- 402	3.29	154.23	H-Bond (Ligand Donor)	false