scPDB - 3upf entry

Protein Data Bank Entry:

PDB ID : 3upf

Resolution :2.600 Å

Experimental Method : X-ray

Deposition Date : 2011-11-18

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Polyprotein
ID:	Q80J95_9CALI
AC:	Q80J95
Organism:	Murine norovirus 1
Reign:	Viruses
TaxID:	223997
EC Number:	/

Chains:

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

Ligand binding site composition:

B-Factor:	46.596
Number of residues:	32
Including
Standard Amino Acids:	31
Non Standard Amino Acids:	0
Water Molecules:	1
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.584	884.250

% Hydrophobic	% Polar
38.17	61.83
According to VolSite

Ligand :

HET Code:	0BU
Formula:	C35H20N4O21S6
Molecular weight:	1024.938 g/mol
DrugBank ID:	-
Buried Surface Area:	37.04 %
Polar Surface area:	492.8 Å2

Number of
H-Bond Acceptors:	21
H-Bond Donors:	4
Rings:	6
Aromatic rings:	6
Anionic atoms:	6
Cationic atoms:	0
Rule of Five Violation:	2
Rotatable Bonds:	12

Mass center Coordinates

X	Y	Z
14.5592	-60.4625	43.5212

Binding mode :

What is Poseview ?

2D View
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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
CBK	CH2	TRP- 42	3.37	0	Hydrophobic	false
CBB	CB	ASP- 65	3.63	0	Hydrophobic	false
OAA	NE2	GLN- 66	2.93	136.76	H-Bond (Protein Donor)	false
CCE	CD	LYS- 68	4.26	0	Hydrophobic	false
CAV	CG	PRO- 69	4.07	0	Hydrophobic	false
CBA	CG1	VAL- 170	3.44	0	Hydrophobic	false
OAO	N	LYS- 171	2.95	170.87	H-Bond (Protein Donor)	false
OAU	NZ	LYS- 174	2.92	144.47	H-Bond (Protein Donor)	false
CBV	CD	LYS- 174	4.23	0	Hydrophobic	false
CAW	CD	LYS- 174	3.99	0	Hydrophobic	false
CBF	CD	LYS- 180	3.7	0	Hydrophobic	false
CAY	CB	LYS- 180	3.84	0	Hydrophobic	false
CBG	CG	ARG- 182	3.83	0	Hydrophobic	false
CAW	CG	ARG- 182	3.62	0	Hydrophobic	false
OAL	CZ	ARG- 245	3.74	0	Ionic (Protein Cationic)	false
OAM	CZ	ARG- 245	3.26	0	Ionic (Protein Cationic)	false
CAV	CD	ARG- 245	3.57	0	Hydrophobic	false