scPDB - 3d5m entry

Protein Data Bank Entry:

PDB ID : 3d5m

Resolution :2.200 Å

Experimental Method : X-ray

Deposition Date : 2008-05-16

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:	39.711
Number of residues:	44
Including
Standard Amino Acids:	41
Non Standard Amino Acids:	0
Water Molecules:	3
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
1.024	1056.375

% Hydrophobic	% Polar
36.74	63.26
According to VolSite

Ligand :

HET Code:	4MS
Formula:	C24H24ClFN3O6S2
Molecular weight:	569.045 g/mol
DrugBank ID:	-
Buried Surface Area:	64.96 %
Polar Surface area:	152.79 Å2

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

Mass center Coordinates

X	Y	Z
96.3094	62.5612	55.5189

Binding mode :

What is Poseview ?

2D View
3D View

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
C23	CZ	PHE- 193	3.86	0	Hydrophobic	false
CL37	CB	PRO- 197	3.65	0	Hydrophobic	false
F34	CB	PRO- 197	3.84	0	Hydrophobic	false
F34	CD	ARG- 200	3.39	0	Hydrophobic	false
C21	CG2	THR- 287	4.15	0	Hydrophobic	false
O32	ND2	ASN- 291	2.83	164.09	H-Bond (Protein Donor)	false
C1	CB	ASN- 316	3.99	0	Hydrophobic	false
O32	N	ASP- 318	3.11	137.34	H-Bond (Protein Donor)	false
C1	CB	ASP- 319	3.93	0	Hydrophobic	false
C1	SG	CYS- 366	3.83	0	Hydrophobic	false
C4	CB	CYS- 366	3.72	0	Hydrophobic	false
CL37	CB	LEU- 384	3.74	0	Hydrophobic	false
F34	CD1	LEU- 384	3.53	0	Hydrophobic	false
C6	CB	MET- 414	4.12	0	Hydrophobic	false
CL37	CB	MET- 414	4.3	0	Hydrophobic	false
C18	CB	MET- 414	4	0	Hydrophobic	false
C20	CG	MET- 414	3.81	0	Hydrophobic	false
C10	CE	MET- 414	3.69	0	Hydrophobic	false
CL37	CE1	TYR- 415	3.98	0	Hydrophobic	false
C18	CE2	TYR- 415	3.65	0	Hydrophobic	false
C20	CG1	ILE- 447	4.42	0	Hydrophobic	false
O33	N	TYR- 448	2.91	167.86	H-Bond (Protein Donor)	false
C21	CB	SER- 556	3.87	0	Hydrophobic	false
C23	CB	SER- 556	3.87	0	Hydrophobic	false