scPDB - 3cde entry

Protein Data Bank Entry:

PDB ID : 3cde

Resolution :2.100 Å

Experimental Method : X-ray

Deposition Date : 2008-02-26

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
A	100 %

Ligand binding site composition:

B-Factor:	28.235
Number of residues:	46
Including
Standard Amino Acids:	44
Non Standard Amino Acids:	0
Water Molecules:	2
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
1.077	1501.875

% Hydrophobic	% Polar
34.83	65.17
According to VolSite

Ligand :

HET Code:	N3H
Formula:	C21H22N5O6S3
Molecular weight:	536.624 g/mol
DrugBank ID:	-
Buried Surface Area:	64.59 %
Polar Surface area:	205.42 Å2

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

Mass center Coordinates

X	Y	Z
95.4946	8.54571	56.8634

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
C17	CG	PRO- 197	4.04	0	Hydrophobic	false
C16	CG	PRO- 197	3.96	0	Hydrophobic	false
C17	CD	ARG- 200	3.91	0	Hydrophobic	false
C18	CG2	THR- 287	4.35	0	Hydrophobic	false
O30	ND2	ASN- 291	2.76	171.59	H-Bond (Protein Donor)	false
C2	CB	ASN- 316	4.01	0	Hydrophobic	false
O30	N	ASP- 318	3.31	138.77	H-Bond (Protein Donor)	false
N26	OD1	ASP- 318	2.62	147.26	H-Bond (Ligand Donor)	false
C3	CB	ASP- 319	4.12	0	Hydrophobic	false
C2	SG	CYS- 366	4.07	0	Hydrophobic	false
C20	CB	CYS- 366	3.9	0	Hydrophobic	false
C19	CB	SER- 368	4.26	0	Hydrophobic	false
C16	CD2	LEU- 384	3.64	0	Hydrophobic	false
C17	CD2	LEU- 384	3.57	0	Hydrophobic	false
S33	CG	MET- 414	3.91	0	Hydrophobic	false
C21	CE	MET- 414	3.66	0	Hydrophobic	false
C20	CZ	TYR- 415	4.4	0	Hydrophobic	false
C16	CZ	TYR- 415	3.82	0	Hydrophobic	false
O32	N	TYR- 448	2.84	144.04	H-Bond (Protein Donor)	false
C17	CE1	TYR- 448	4.32	0	Hydrophobic	false
C5	CB	SER- 556	3.87	0	Hydrophobic	false
C18	CB	SER- 556	3.73	0	Hydrophobic	false