scPDB - 1nb6 entry

Protein Data Bank Entry:

PDB ID : 1nb6

Resolution :2.600 Å

Experimental Method : X-ray

Deposition Date : 2002-12-02

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Genome polyprotein
ID:	POLG_HCVJ4
AC:	O92972
Organism:	Hepatitis C virus genotype 1b
Reign:	Viruses
TaxID:	420174
EC Number:	2.7.7.48

Chains:

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

Ligand binding site composition:

B-Factor:	28.933
Number of residues:	33
Including
Standard Amino Acids:	31
Non Standard Amino Acids:	2
Water Molecules:	0
Cofactors:
Metals:	MN MN

Cavity properties

Ligandability	Volume (Å3)
0.671	1248.750

% Hydrophobic	% Polar
25.95	74.05
According to VolSite

Ligand :

HET Code:	UTP
Formula:	C9H11N2O15P3
Molecular weight:	480.109 g/mol
DrugBank ID:	DB04005
Buried Surface Area:	48.01 %
Polar Surface area:	299.67 Å2

Number of
H-Bond Acceptors:	15
H-Bond Donors:	3
Rings:	2
Aromatic rings:	0
Anionic atoms:	4
Cationic atoms:	0
Rule of Five Violation:	1
Rotatable Bonds:	8

Mass center Coordinates

X	Y	Z
14.9998	60.131	55.3433

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
O1G	CZ	ARG- 48	3.21	0	Ionic (Protein Cationic)	false
O1B	N	CYS- 223	3.18	136.08	H-Bond (Protein Donor)	false
C4'	CB	PHE- 224	4.17	0	Hydrophobic	false
O2'	N	ASP- 225	3.42	142.01	H-Bond (Protein Donor)	false
C1'	CB	ASP- 225	3.94	0	Hydrophobic	false
O4	OG	SER- 556	3.05	140.19	H-Bond (Protein Donor)	false
O1A	MN	MN- 1002	2.03	0	Metal Acceptor	false
O1B	MN	MN- 1002	2.22	0	Metal Acceptor	false