scPDB - 5dto entry

Protein Data Bank Entry:

PDB ID : 5dto

Resolution :2.600 Å

Experimental Method : X-ray

Deposition Date : 2015-09-18

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:	Q6DLV0_9FLAV
AC:	Q6DLV0
Organism:	Dengue virus 3
Reign:	Viruses
TaxID:	11069
EC Number:	/

Chains:

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

Ligand binding site composition:

B-Factor:	33.308
Number of residues:	37
Including
Standard Amino Acids:	35
Non Standard Amino Acids:	0
Water Molecules:	2
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.380	388.125

% Hydrophobic	% Polar
50.43	49.57
According to VolSite

Ligand :

HET Code:	SAH
Formula:	C14H20N6O5S
Molecular weight:	384.411 g/mol
DrugBank ID:	DB01752
Buried Surface Area:	65.55 %
Polar Surface area:	212.38 Å2

Number of
H-Bond Acceptors:	10
H-Bond Donors:	4
Rings:	3
Aromatic rings:	2
Anionic atoms:	1
Cationic atoms:	1
Rule of Five Violation:	1
Rotatable Bonds:	7

Mass center Coordinates

X	Y	Z
20.4582	129.448	15.8778

Binding mode :

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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
OXT	OG	SER- 56	2.93	147.82	H-Bond (Protein Donor)	false
OXT	N	GLY- 86	3.04	149.25	H-Bond (Protein Donor)	false
N3	N	LYS- 105	2.98	128.81	H-Bond (Protein Donor)	false
O2'	ND1	HIS- 110	3.14	166.76	H-Bond (Ligand Donor)	false
C3'	CG	GLU- 111	4.4	0	Hydrophobic	false
O2'	N	GLU- 111	3.43	144.89	H-Bond (Protein Donor)	false
N6	OD1	ASP- 131	2.59	152.43	H-Bond (Ligand Donor)	false
N1	N	VAL- 132	3.15	160.26	H-Bond (Protein Donor)	false
N	OD2	ASP- 146	2.76	137.03	H-Bond (Ligand Donor)	false
N	OD2	ASP- 146	2.76	0	Ionic (Ligand Cationic)	false
CG	CB	ASP- 146	3.88	0	Hydrophobic	false