scPDB - 4oav entry

Protein Data Bank Entry:

PDB ID : 4oav

Resolution :2.100 Å

Experimental Method : X-ray

Deposition Date : 2014-01-06

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
D	100 %

Ligand binding site composition:

B-Factor:	48.964
Number of residues:	37
Including
Standard Amino Acids:	34
Non Standard Amino Acids:	2
Water Molecules:	1
Cofactors:
Metals:	MG MG

Cavity properties

Ligandability	Volume (Å3)
1.228	469.125

% Hydrophobic	% Polar
64.75	35.25
According to VolSite

Ligand :

HET Code:	ACP
Formula:	C11H14N5O12P3
Molecular weight:	501.176 g/mol
DrugBank ID:	DB03909
Buried Surface Area:	57.32 %
Polar Surface area:	310.64 Å2

Number of
H-Bond Acceptors:	16
H-Bond Donors:	3
Rings:	3
Aromatic rings:	2
Anionic atoms:	4
Cationic atoms:	0
Rule of Five Violation:	2
Rotatable Bonds:	8

Mass center Coordinates

X	Y	Z
6.12781	17.4858	75.2386

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
C1'	CG2	ILE- 371	3.99	0	Hydrophobic	false
C1'	CB	ALA- 372	4.13	0	Hydrophobic	false
C4'	CB	ALA- 372	3.68	0	Hydrophobic	false
C3B	CB	THR- 374	4.18	0	Hydrophobic	false
O2G	N	SER- 375	3.06	126.58	H-Bond (Protein Donor)	false
C1'	CG1	ILE- 379	4.27	0	Hydrophobic	false
C5'	CG1	ILE- 379	3.99	0	Hydrophobic	false
O1B	NZ	LYS- 392	2.91	154.35	H-Bond (Protein Donor)	false
O2A	NZ	LYS- 392	2.67	167.11	H-Bond (Protein Donor)	false
O1B	NZ	LYS- 392	2.91	0	Ionic (Protein Cationic)	false
O2A	NZ	LYS- 392	2.67	0	Ionic (Protein Cationic)	false
O1G	CZ	ARG- 400	3.57	0	Ionic (Protein Cationic)	false
O1G	NH2	ARG- 400	3.36	131.77	H-Bond (Protein Donor)	false
O1G	NH1	ARG- 400	2.95	147.53	H-Bond (Protein Donor)	false
N6	O	THR- 435	2.77	161.72	H-Bond (Ligand Donor)	false
N1	N	CYS- 437	3.02	162.21	H-Bond (Protein Donor)	false
C2'	CG2	THR- 440	3.67	0	Hydrophobic	false
O3'	O	GLN- 489	2.81	166.01	H-Bond (Ligand Donor)	false
C2'	CD2	LEU- 492	4.22	0	Hydrophobic	false
O2B	MG	MG- 1002	2.13	0	Metal Acceptor	false
O1A	MG	MG- 1002	2.02	0	Metal Acceptor	false
O1B	MG	MG- 1003	2.04	0	Metal Acceptor	false