scPDB - 2r8f entry

Protein Data Bank Entry:

PDB ID : 2r8f

Resolution :2.800 Å

Experimental Method : X-ray

Deposition Date : 2007-09-10

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Non-structural protein 2
ID:	NSP2_ROTSR
AC:	Q03243
Organism:	Rotavirus A )
Reign:	Viruses
TaxID:	36435
EC Number:	3.6.4

Chains:

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

Ligand binding site composition:

B-Factor:	60.799
Number of residues:	26
Including
Standard Amino Acids:	25
Non Standard Amino Acids:	0
Water Molecules:	1
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.660	1134.000

% Hydrophobic	% Polar
35.42	64.58
According to VolSite

Ligand :

HET Code:	AGS
Formula:	C10H14N5O12P3S
Molecular weight:	521.231 g/mol
DrugBank ID:	DB02930
Buried Surface Area:	37.41 %
Polar Surface area:	329.24 Å2

Number of
H-Bond Acceptors:	17
H-Bond Donors:	5
Rings:	3
Aromatic rings:	2
Anionic atoms:	2
Cationic atoms:	0
Rule of Five Violation:	2
Rotatable Bonds:	8

Mass center Coordinates

X	Y	Z
-16.6067	44.8784	15.2341

Binding mode :

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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
N1	NH2	ARG- 109	3.3	144.7	H-Bond (Protein Donor)	false
O3G	NZ	LYS- 188	3.17	167.05	H-Bond (Protein Donor)	false
O3G	NZ	LYS- 188	3.17	0	Ionic (Protein Cationic)	false
O2B	NZ	LYS- 223	2.68	170.39	H-Bond (Protein Donor)	false
O2B	NZ	LYS- 223	2.68	0	Ionic (Protein Cationic)	false
O3G	CZ	ARG- 227	3.97	0	Ionic (Protein Cationic)	false
O1A	CZ	ARG- 227	3.74	0	Ionic (Protein Cationic)	false
C5'	CD	ARG- 240	4.3	0	Hydrophobic	false
C3'	CB	ARG- 240	3.8	0	Hydrophobic	false
C1'	CD	ARG- 240	3.47	0	Hydrophobic	false
O3'	OG1	THR- 244	2.74	153.65	H-Bond (Ligand Donor)	false
O2G	O	HOH- 436	3.14	135.14	H-Bond (Protein Donor)	false