scPDB - 4o1p entry

Protein Data Bank Entry:

PDB ID : 4o1p

Resolution :2.500 Å

Experimental Method : X-ray

Deposition Date : 2013-12-16

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Ribonuclease L
ID:	A5H025_PIG
AC:	A5H025
Organism:	Sus scrofa
Reign:	Eukaryota
TaxID:	9823
EC Number:	/

Chains:

Chain Name:	Percentage of Residues within binding site
A	71 %
B	29 %

Ligand binding site composition:

B-Factor:	51.591
Number of residues:	52
Including
Standard Amino Acids:	49
Non Standard Amino Acids:	0
Water Molecules:	3
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.751	1329.750

% Hydrophobic	% Polar
38.32	61.68
According to VolSite

Ligand :

HET Code:	25L
Formula:	C30H34N15O25P5
Molecular weight:	1159.545 g/mol
DrugBank ID:	-
Buried Surface Area:	47.37 %
Polar Surface area:	654.83 Å2

Number of
H-Bond Acceptors:	37
H-Bond Donors:	7
Rings:	9
Aromatic rings:	6
Anionic atoms:	6
Cationic atoms:	0
Rule of Five Violation:	3
Rotatable Bonds:	20

Mass center Coordinates

X	Y	Z
3.87343	18.8334	48.5692

Binding mode :

What is Poseview ?

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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
C4'	CD2	TRP- 56	3.78	0	Hydrophobic	false
O4'	NE1	TRP- 58	3.47	137.02	H-Bond (Protein Donor)	false
N6	OG	SER- 63	3.4	143.71	H-Bond (Ligand Donor)	false
N6	OE1	GLN- 66	2.84	152.71	H-Bond (Ligand Donor)	false
N7	NE2	GLN- 66	3.23	161.99	H-Bond (Protein Donor)	false
OAF	NZ	LYS- 87	3.97	0	Ionic (Protein Cationic)	false
OAP	NZ	LYS- 87	3.02	0	Ionic (Protein Cationic)	false
OAP	NZ	LYS- 87	3.02	126.36	H-Bond (Protein Donor)	false
CCJ	CB	ASN- 89	3.97	0	Hydrophobic	false
CCI	CB	ASN- 122	4.13	0	Hydrophobic	false
CCN	CE2	PHE- 124	4.32	0	Hydrophobic	false
DuAr	DuAr	PHE- 124	3.57	0	Aromatic Face/Face	false
NAB	OE1	GLU- 129	3.14	146.54	H-Bond (Ligand Donor)	false
NBC	OE1	GLU- 129	3.38	139.22	H-Bond (Ligand Donor)	false
NBC	OE2	GLU- 129	2.81	140.13	H-Bond (Ligand Donor)	false
NAC	OH	TYR- 133	3.17	121.54	H-Bond (Ligand Donor)	false
NBD	OH	TYR- 133	2.56	163.36	H-Bond (Protein Donor)	false
OAE	NH2	ARG- 153	3.35	135.53	H-Bond (Protein Donor)	false
OAM	NH2	ARG- 153	3.06	137.69	H-Bond (Protein Donor)	false
OAM	NE	ARG- 153	2.78	157.42	H-Bond (Protein Donor)	false
OAM	CZ	ARG- 153	3.35	0	Ionic (Protein Cationic)	false
OAD	NZ	LYS- 164	2.55	133.85	H-Bond (Protein Donor)	false
OAR	NZ	LYS- 164	3.01	140.38	H-Bond (Protein Donor)	false
OAD	NZ	LYS- 164	2.55	0	Ionic (Protein Cationic)	false
OAR	NZ	LYS- 164	3.01	0	Ionic (Protein Cationic)	false
DuAr	CZ	ARG- 307	3.75	166.64	Pi/Cation	false
C3'	CG	ARG- 308	3.65	0	Hydrophobic	false
OAF	OH	TYR- 310	2.61	163.53	H-Bond (Protein Donor)	false
OAG	CZ	ARG- 353	3.83	0	Ionic (Protein Cationic)	false
OAQ	CZ	ARG- 353	3.66	0	Ionic (Protein Cationic)	false
OAQ	NH1	ARG- 353	3.37	141.1	H-Bond (Protein Donor)	false
OAQ	NH2	ARG- 353	3.04	161.05	H-Bond (Protein Donor)	false
CBA	CE1	PHE- 362	4.22	0	Hydrophobic	false
NBF	O	HOH- 1002	2.98	161.25	H-Bond (Protein Donor)	false