scPDB - 4g8l entry

Protein Data Bank Entry:

PDB ID : 4g8l

Resolution :2.800 Å

Experimental Method : X-ray

Deposition Date : 2012-07-23

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	2-5A-dependent ribonuclease
ID:	RN5A_HUMAN
AC:	Q05823
Organism:	Homo sapiens
Reign:	Eukaryota
TaxID:	9606
EC Number:	3.1.26

Chains:

Chain Name:	Percentage of Residues within binding site
A	20 %
B	78 %
C	2 %

Ligand binding site composition:

B-Factor:	65.713
Number of residues:	41
Including
Standard Amino Acids:	41
Non Standard Amino Acids:	0
Water Molecules:	0
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.345	580.500

% Hydrophobic	% Polar
44.19	55.81
According to VolSite

Ligand :

HET Code:	25A
Formula:	C30H34N15O19P3
Molecular weight:	1001.601 g/mol
DrugBank ID:	-
Buried Surface Area:	52.13 %
Polar Surface area:	536.5 Å2

Number of
H-Bond Acceptors:	31
H-Bond Donors:	7
Rings:	9
Aromatic rings:	6
Anionic atoms:	4
Cationic atoms:	0
Rule of Five Violation:	3
Rotatable Bonds:	16

Mass center Coordinates

X	Y	Z
-1.06687	-68.1927	29.8428

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
CL'	CG	GLU- 57	3.7	0	Hydrophobic	false
OLP	NE1	TRP- 60	2.94	120.93	H-Bond (Protein Donor)	false
DuAr	DuAr	TRP- 60	3.76	0	Aromatic Face/Face	false
N26	OD1	ASN- 65	2.87	125.87	H-Bond (Ligand Donor)	false
N21	NE2	GLN- 68	2.95	159.37	H-Bond (Protein Donor)	false
N26	OE1	GLN- 68	2.82	154.49	H-Bond (Ligand Donor)	false
OLP	NZ	LYS- 89	2.61	153.13	H-Bond (Protein Donor)	false
OLP	NZ	LYS- 89	2.61	0	Ionic (Protein Cationic)	false
OMP	NZ	LYS- 89	3.96	0	Ionic (Protein Cationic)	false
CE'	CB	ASN- 91	3.96	0	Hydrophobic	false
CC'	CB	ASN- 91	4.35	0	Hydrophobic	false
C4'	CD1	TYR- 124	3.77	0	Hydrophobic	false
CF'	CE2	TYR- 124	3.86	0	Hydrophobic	false
C1'	CE2	PHE- 126	4.49	0	Hydrophobic	false
C5'	CE2	PHE- 126	3.87	0	Hydrophobic	false
DuAr	DuAr	PHE- 126	3.55	0	Aromatic Face/Face	false
N6	OE1	GLU- 131	2.86	162.72	H-Bond (Ligand Donor)	false
N1	OE1	GLU- 131	3.48	132.02	H-Bond (Ligand Donor)	false
O2P	NE	ARG- 155	2.69	167.12	H-Bond (Protein Donor)	false
O2P	NH2	ARG- 155	3.36	128.07	H-Bond (Protein Donor)	false
O3P	NH2	ARG- 155	2.89	158.28	H-Bond (Protein Donor)	false
O2P	CZ	ARG- 155	3.44	0	Ionic (Protein Cationic)	false
O3P	CZ	ARG- 155	3.83	0	Ionic (Protein Cationic)	false
CM'	CE	MET- 306	4.15	0	Hydrophobic	false
CM'	CG	ARG- 310	3.62	0	Hydrophobic	false
OMP	OH	TYR- 312	2.75	149.65	H-Bond (Protein Donor)	false