scPDB - 3gyn entry

Protein Data Bank Entry:

PDB ID : 3gyn

Resolution :2.150 Å

Experimental Method : X-ray

Deposition Date : 2009-04-04

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_HCVBK
AC:	P26663
Organism:	Hepatitis C virus genotype 1b
Reign:	Viruses
TaxID:	11105
EC Number:	2.7.7.48

Chains:

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

Ligand binding site composition:

B-Factor:	37.344
Number of residues:	47
Including
Standard Amino Acids:	45
Non Standard Amino Acids:	0
Water Molecules:	2
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.909	1147.500

% Hydrophobic	% Polar
31.76	68.24
According to VolSite

Ligand :

HET Code:	B42
Formula:	C24H33N4O6S2
Molecular weight:	537.672 g/mol
DrugBank ID:	-
Buried Surface Area:	60.79 %
Polar Surface area:	164.83 Å2

Number of
H-Bond Acceptors:	8
H-Bond Donors:	2
Rings:	4
Aromatic rings:	1
Anionic atoms:	1
Cationic atoms:	0
Rule of Five Violation:	1
Rotatable Bonds:	7

Mass center Coordinates

X	Y	Z
53.4396	-8.31811	51.0579

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
C19	CG	PRO- 197	3.85	0	Hydrophobic	false
C20	CD	ARG- 200	3.76	0	Hydrophobic	false
C21	CG2	THR- 287	4.2	0	Hydrophobic	false
O32	ND2	ASN- 291	2.82	160.86	H-Bond (Protein Donor)	false
C1	CB	ASN- 316	4.45	0	Hydrophobic	false
O32	N	ASP- 318	3.33	128.38	H-Bond (Protein Donor)	false
N28	OD1	ASP- 318	2.73	147.47	H-Bond (Ligand Donor)	false
C2	CB	ASP- 319	4.16	0	Hydrophobic	false
C1	SG	CYS- 366	4.28	0	Hydrophobic	false
C23	CB	CYS- 366	4.18	0	Hydrophobic	false
C20	CB	CYS- 366	4.39	0	Hydrophobic	false
C18	CB	SER- 367	4	0	Hydrophobic	false
C19	CD2	LEU- 384	3.65	0	Hydrophobic	false
C13	CG	MET- 414	3.68	0	Hydrophobic	false
C24	CE	MET- 414	3.91	0	Hydrophobic	false
C22	CZ	TYR- 415	4.31	0	Hydrophobic	false
C19	CZ	TYR- 415	3.89	0	Hydrophobic	false
O29	N	TYR- 448	2.82	135.59	H-Bond (Protein Donor)	false
C24	CE1	TYR- 448	3.96	0	Hydrophobic	false
C21	CB	SER- 556	3.71	0	Hydrophobic	false
C3	CB	SER- 556	3.94	0	Hydrophobic	false
O30	OG	SER- 556	3.35	130.41	H-Bond (Protein Donor)	false