scPDB - 3n6m entry

Protein Data Bank Entry:

PDB ID : 3n6m

Resolution :2.500 Å

Experimental Method : X-ray

Deposition Date : 2010-05-26

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:	D3K0N8_9ENTO
AC:	D3K0N8
Organism:	Enterovirus A71
Reign:	Viruses
TaxID:	39054
EC Number:	/

Chains:

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

Ligand binding site composition:

B-Factor:	37.735
Number of residues:	25
Including
Standard Amino Acids:	25
Non Standard Amino Acids:	0
Water Molecules:	0
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.170	641.250

% Hydrophobic	% Polar
40.00	60.00
According to VolSite

Ligand :

HET Code:	GTP
Formula:	C10H12N5O14P3
Molecular weight:	519.149 g/mol
DrugBank ID:	DB04137
Buried Surface Area:	46.46 %
Polar Surface area:	335.56 Å2

Number of
H-Bond Acceptors:	17
H-Bond Donors:	4
Rings:	3
Aromatic rings:	1
Anionic atoms:	4
Cationic atoms:	0
Rule of Five Violation:	2
Rotatable Bonds:	8

Mass center Coordinates

X	Y	Z
-37.0419	21.3426	13.9723

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
O1A	NH2	ARG- 163	3.48	133.51	H-Bond (Protein Donor)	false
O1A	NH1	ARG- 163	2.94	160.96	H-Bond (Protein Donor)	false
O2A	NH2	ARG- 163	2.9	153.65	H-Bond (Protein Donor)	false
O1A	CZ	ARG- 163	3.65	0	Ionic (Protein Cationic)	false
O2A	CZ	ARG- 163	3.79	0	Ionic (Protein Cationic)	false
O1G	NZ	LYS- 167	3.83	0	Ionic (Protein Cationic)	false
O3G	NZ	LYS- 167	3.55	0	Ionic (Protein Cationic)	false
O1A	NZ	LYS- 167	3.93	0	Ionic (Protein Cationic)	false
C5'	CD	ARG- 174	3.66	0	Hydrophobic	false
O4'	NH1	ARG- 174	3.07	136.04	H-Bond (Protein Donor)	false
N1	O	LEU- 175	2.76	147.14	H-Bond (Ligand Donor)	false
N2	O	LEU- 175	3.01	136.26	H-Bond (Ligand Donor)	false
O2G	OG	SER- 235	2.86	165.9	H-Bond (Protein Donor)	false
O2B	N	GLY- 236	2.64	163.19	H-Bond (Protein Donor)	false
O3'	N	ASP- 238	3.35	152.85	H-Bond (Protein Donor)	false
C2'	CB	ASP- 238	4.35	0	Hydrophobic	false